Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)

PubMed Central

Nayak, Spurthi N.; Varghese, Nicy; Shah, Trushar M.; Penmetsa, R. Varma; Thirunavukkarasu, Nepolean; Gudipati, Srivani; Gaur, Pooran M.; Kulwal, Pawan L.; Upadhyaya, Hari D.; KaviKishor, Polavarapu B.; Winter, Peter; Kahl, Günter; Town, Christopher D.; Kilian, Andrzej; Cook, Douglas R.; Varshney, Rajeev K.

2011-01-01

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes. PMID:22102885

Segmental Duplications and Copy-Number Variation in the Human Genome

PubMed Central

Sharp, Andrew J. ; Locke, Devin P. ; McGrath, Sean D. ; Cheng, Ze ; Bailey, Jeffrey A. ; Vallente, Rhea U. ; Pertz, Lisa M. ; Clark, Royden A. ; Schwartz, Stuart ; Segraves, Rick ; Oseroff, Vanessa V. ; Albertson, Donna G. ; Pinkel, Daniel ; Eichler, Evan E. 

2005-01-01

The human genome contains numerous blocks of highly homologous duplicated sequence. This higher-order architecture provides a substrate for recombination and recurrent chromosomal rearrangement associated with genomic disease. However, an assessment of the role of segmental duplications in normal variation has not yet been made. On the basis of the duplication architecture of the human genome, we defined a set of 130 potential rearrangement hotspots and constructed a targeted bacterial artificial chromosome (BAC) microarray (with 2,194 BACs) to assess copy-number variation in these regions by array comparative genomic hybridization. Using our segmental duplication BAC microarray, we screened a panel of 47 normal individuals, who represented populations from four continents, and we identified 119 regions of copy-number polymorphism (CNP), 73 of which were previously unreported. We observed an equal frequency of duplications and deletions, as well as a 4-fold enrichment of CNPs within hotspot regions, compared with control BACs (P < .000001), which suggests that segmental duplications are a major catalyst of large-scale variation in the human genome. Importantly, segmental duplications themselves were also significantly enriched >4-fold within regions of CNP. Almost without exception, CNPs were not confined to a single population, suggesting that these either are recurrent events, having occurred independently in multiple founders, or were present in early human populations. Our study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and it suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements. Our specialized segmental duplication BAC microarray and associated database of structural polymorphisms will provide an important resource for the future characterization of human genomic disorders. PMID:15918152

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

PubMed Central

Menten, Björn; Pattyn, Filip; De Preter, Katleen; Robbrecht, Piet; Michels, Evi; Buysse, Karen; Mortier, Geert; De Paepe, Anne; van Vooren, Steven; Vermeesch, Joris; Moreau, Yves; De Moor, Bart; Vermeulen, Stefan; Speleman, Frank; Vandesompele, Jo

2005-01-01

Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at . PMID:15910681

Evaluation of Genomic Instability in the Abnormal Prostate

DTIC Science & Technology

2006-12-01

array CGH maps copy number aberrations relative to the genome sequence by using arrays of BAC or cDNA clones as the hybridization target instead of...data produced from these analyses complicate the interpretation of results . For these reasons, and as outlined by Davies et al., 22 it is desirable...There have been numerous studies of these abnormalities and several techniques, including 9 chromosome painting, array CGH and SNP arrays , have

Comparative activity and mechanism of action of three types of bovine antimicrobial peptides against pathogenic Prototheca spp.

PubMed

Tomasinsig, Linda; Skerlavaj, Barbara; Scarsini, Michele; Guida, Filomena; Piccinini, Renata; Tossi, Alessandro; Zanetti, Margherita

2012-02-01

The yeast-like algae of the genus Prototheca are ubiquitous saprophytes causing infections in immunocompromised patients and granulomatous mastitis in cattle. Few available therapies and the rapid spread of resistant strains worldwide support the need for novel drugs against protothecosis. Host defence antimicrobial peptides inactivate a wide array of pathogens and are a rich source of leads, with the advantage of being largely unaffected by microbial resistance mechanisms. Three structurally diverse bovine peptides [BMAP-28, Bac5 and lingual antimicrobial peptide (LAP)] have thus been tested for their capacity to inactivate Prototheca spp. In minimum inhibitory concentration (MIC) assays, they were all effective in the micromolar range against clinical mastitis isolates as well as a Prototheca wickerhamii reference strain. BMAP-28 sterilized Prototheca cultures within 30-60 min at its MIC, induced cell permeabilization with near 100% release of cellular adenosine triphosphate and resulted in extensive surface blebbing and release of intracellular material as observed by scanning electron microscopy. Bac5 and LAP inactivated Prototheca following 3-6 h incubation at fourfold their MIC and did not result in detectable surface damage despite 70-90% killing, suggesting they act via non-lytic mechanisms. In circular dichroism studies, the conformation of BMAP-28, but not that of Bac5 or LAP, was affected by interaction with liposomes mimicking algal membranes. Our results indicate that BMAP-28, Bac5 and LAP kill Prototheca with distinct potencies, killing kinetics, and modes of action and may be appropriate for protothecal mastitis treatment. In addition, the ability of Bac5 and LAP to act via non-lytic mechanisms may be exploited for the development of target-selective drugs. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.

Genome profiling of ovarian adenocarcinomas using pangenomic BACs microarray comparative genomic hybridization

PubMed Central

Caserta, Donatella; Benkhalifa, Moncef; Baldi, Marina; Fiorentino, Francesco; Qumsiyeh, Mazin; Moscarini, Massimo

2008-01-01

Background Routine cytogenetic investigations for ovarian cancers are limited by culture failure and poor growth of cancer cells compared to normal cells. Fluorescence in situ Hybridization (FISH) application or classical comparative genome hybridization techniques are also have their own limitations in detecting genome imbalance especially for small changes that are not known ahead of time and for which FISH probes could not be thus designed. Methods We applied microarray comparative genomic hybridization (A-CGH) using one mega base BAC arrays to investigate chromosomal disorders in ovarian adenocarcinoma in patients with familial history. Results Our data on 10 cases of ovarian cancer revealed losses of 6q (4 cases mainly mosaic loss), 9p (4 cases), 10q (3 cases), 21q (3 cases), 22q (4 cases) with association to a monosomy X and gains of 8q and 9q (occurring together in 8 cases) and gain of 12p. There were other abnormalities such as loss of 17p that were noted in two profiles of the studied cases. Total or mosaic segmental gain of 2p, 3q, 4q, 7q and 13q were also observed. Seven of 10 patients were investigated by FISH to control array CGH results. The FISH data showed a concordance between the 2 methods. Conclusion The data suggest that A-CGH detects unique and common abnormalities with certain exceptions such as tetraploidy and balanced translocation, which may lead to understanding progression of genetic changes as well as aid in early diagnosis and have an impact on therapy and prognosis. PMID:18492273

Synteny of Prunus and other model plant species

PubMed Central

Jung, Sook; Jiwan, Derick; Cho, Ilhyung; Lee, Taein; Abbott, Albert; Sosinski, Bryon; Main, Dorrie

2009-01-01

Background Fragmentary conservation of synteny has been reported between map-anchored Prunus sequences and Arabidopsis. With the availability of genome sequence for fellow rosid I members Populus and Medicago, we analyzed the synteny between Prunus and the three model genomes. Eight Prunus BAC sequences and map-anchored Prunus sequences were used in the comparison. Results We found a well conserved synteny across the Prunus species – peach, plum, and apricot – and Populus using a set of homologous Prunus BACs. Conversely, we could not detect any synteny with Arabidopsis in this region. Other peach BACs also showed extensive synteny with Populus. The syntenic regions detected were up to 477 kb in Populus. Two syntenic regions between Arabidopsis and these BACs were much shorter, around 10 kb. We also found syntenic regions that are conserved between the Prunus BACs and Medicago. The array of synteny corresponded with the proposed whole genome duplication events in Populus and Medicago. Using map-anchored Prunus sequences, we detected many syntenic blocks with several gene pairs between Prunus and Populus or Arabidopsis. We observed a more complex network of synteny between Prunus-Arabidopsis, indicative of multiple genome duplication and subsequence gene loss in Arabidopsis. Conclusion Our result shows the striking microsynteny between the Prunus BACs and the genome of Populus and Medicago. In macrosynteny analysis, more distinct Prunus regions were syntenic to Populus than to Arabidopsis. PMID:19208249

Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes

PubMed Central

Howarth, KD; Blood, KA; Ng, BL; Beavis, JC; Chua, Y; Cooke, SL; Raby, S; Ichimura, K; Collins, VP; Carter, NP; Edwards, PAW

2008-01-01

Chromosome translocations in the common epithelial cancers are abundant, yet little is known about them. They have been thought to be almost all unbalanced and therefore dismissed as mostly mediating tumour suppressor loss. We present a comprehensive analysis by array painting of the chromosome translocations of breast cancer cell lines HCC1806, HCC1187 and ZR-75-30. In array painting, chromosomes are isolated by flow cytometry, amplified and hybridized to DNA microarrays. A total of 200 breakpoints were identified and all were mapped to 1Mb resolution on BAC arrays, then 40 selected breakpoints, including all balanced breakpoints, were further mapped on tiling-path BAC arrays or to around 2kb resolution using oligonucleotide arrays. Many more of the translocations were balanced at 1Mb resolution than expected, either reciprocal (eight in total) or balanced for at least one participating chromosome (19 paired breakpoints). Secondly, many of the breakpoints were at genes that are plausible targets of oncogenic translocation, including balanced breaks at CTCF, EP300/p300, and FOXP4. Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer. PMID:18084325

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

PubMed Central

2010-01-01

Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish. PMID:20105308

Effects of dietary benzoic acid and sodium-benzoate on performance, nitrogen and mineral balance and hippuric acid excretion of piglets.

PubMed

Gräber, Tobias; Kluge, Holger; Hirche, Frank; Broz, Jirí; Stangl, Gabriele I

2012-06-01

The objective of this study was to compare the effects of sodium-benzoate (NaB) with those of benzoic acid (BAc) on growth performance of piglets as well as nutrient digestibility, nitrogen and mineral balance, urinary pH, and the urinary excretion of BAc and hippuric acid (HAc). The study was conducted with 120 weaning piglets (6.5 kg body weight), divided in four groups (15 replicates of two piglets each), which received (1) a basal diet (Control), or the basal diet supplemented with (2) 4 g NaB per kg (Group 4NaB), (3) 3.5 g BAc per kg (Group 3.5BAc) or (4) 5 g BAc per kg (Group 5BAc). Performance data were monitored over a 42-day period. Urine and faeces were collected from day 28-33 in metabolic cages with five piglets per treatment. Piglets of Groups 3.5BAc and 5BAc had similarly a considerably improved average daily gain and feed intake (p < 0.05). Performance of Group 4NaB was not significantly different from the other groups. Compared to the Control, the nitrogen retention was only improved in Group 5BAc (p < 0.05); the other groups showed intermediate values. In the supplemented groups, most of the BAc was excreted as HAc in urine, but only Groups 3.5BAc and 5BAc had reduced urinary pH (p < 0.05). Daily intake and faecal and urinary excretion of P and Ca were not affected by the treatment. The molar excess of Na in Group 4NaB was reflected by higher renal excretion of Na compared to the other groups (p < 0.05).

Cloning of the koi herpesvirus genome as an infectious bacterial artificial chromosome demonstrates that disruption of the thymidine kinase locus induces partial attenuation in Cyprinus carpio koi.

PubMed

Costes, B; Fournier, G; Michel, B; Delforge, C; Raj, V Stalin; Dewals, B; Gillet, L; Drion, P; Body, A; Schynts, F; Lieffrig, F; Vanderplasschen, A

2008-05-01

Koi herpesvirus (KHV) is the causative agent of a lethal disease in koi and common carp. In the present study, we describe the cloning of the KHV genome as a stable and infectious bacterial artificial chromosome (BAC) clone that can be used to produce KHV recombinant strains. This goal was achieved by the insertion of a loxP-flanked BAC cassette into the thymidine kinase (TK) locus. This insertion led to a BAC plasmid that was stably maintained in bacteria and was able to regenerate virions when permissive cells were transfected with the plasmid. Reconstituted virions free of the BAC cassette but carrying a disrupted TK locus (the FL BAC-excised strain) were produced by the transfection of Cre recombinase-expressing cells with the BAC. Similarly, virions with a wild-type revertant TK sequence (the FL BAC revertant strain) were produced by the cotransfection of cells with the BAC and a DNA fragment encoding the wild-type TK sequence. Reconstituted recombinant viruses were compared to the wild-type parental virus in vitro and in vivo. The FL BAC revertant strain and the FL BAC-excised strain replicated comparably to the parental FL strain. The FL BAC revertant strain induced KHV infection in koi carp that was indistinguishable from that induced by the parental strain, while the FL BAC-excised strain exhibited a partially attenuated phenotype. Finally, the usefulness of the KHV BAC for recombination studies was demonstrated by the production of an ORF16-deleted strain by using prokaryotic recombination technology. The availability of the KHV BAC is an important advance that will allow the study of viral genes involved in KHV pathogenesis, as well as the production of attenuated recombinant candidate vaccines.

Comparison of biological activated carbon (BAC) and membrane bioreactor (MBR) for pollutants removal in drinking water treatment.

PubMed

Tian, J Y; Chen, Z L; Liang, H; Li, X; Wang, Z Z; Li, G B

2009-01-01

Biological activated carbon (BAC) and membrane bioreactor (MBR) were systematically compared for the drinking water treatment from slightly polluted raw water under the same hydraulic retention time (HRT) of 0.5 h. MBR exhibited excellent turbidity removal capacity due to the separation of the membrane; while only 60% of influent turbidity was intercepted by BAC. Perfect nitrification was achieved by MBR with the 89% reduction in ammonia; by contrast, BAC only eliminated a moderate amount of influent ammonia (by 54.5%). However, BAC was able to remove more dissolved organic matter (DOM, especially for organic molecules of 3,000 approximately 500 Daltons) and corresponding disinfection by-product formation potential (DBPFP) in raw water than MBR. Unfortunately, particulate organic matter (POM) was detected in the BAC effluent. On the other hand, BAC and MBR displayed essentially the same capacity for biodegradable organic matter (BOM) removal. Fractionation of DOM showed that the removal efficiencies of hydrophobic neutrals, hydrophobic acids, weakly hydrophobic acids and hydrophilic organic matter through BAC treatment were 11.7%, 8.8%, 13.9% and 4.8% higher than that through MBR; while MBR achieved 13.8% higher hydrophobic bases removal as compared with BAC.

A controlled comparison of the BacT/ALERT® 3D and VIRTUO™ microbial detection systems.

PubMed

Totty, H; Ullery, M; Spontak, J; Viray, J; Adamik, M; Katzin, B; Dunne, W M; Deol, P

2017-10-01

The performance of the next-generation BacT/ALERT® VIRTUO™ Microbial Detection System (VIRTUO™, bioMérieux Inc., Hazelwood, MO) was compared to the BacT/ALERT® 3D Microbial Detection System (3D, bioMérieux Inc., Durham, NC) using BacT/ALERT® FA Plus (FA Plus), BacT/ALERT® PF Plus (PF Plus), BacT/ALERT® FN Plus (FN Plus), BacT/ALERT® Standard Aerobic (SA), and BacT/ALERT® Standard Anaerobic (SN) blood culture bottles (bioMérieux Inc., Durham, NC). A seeded limit of detection (LoD) study was performed for each bottle type in both systems. The LoD studies demonstrated that both systems were capable of detecting organisms at nearly identical levels [<10 colony-forming units (CFU) per bottle], with no significant difference. Following LoD determination, a seeded study was performed to compare the time to detection (TTD) between the systems using a panel of clinically relevant microorganisms inoculated at or near the LoD with 0, 4, or 10 mL of healthy human blood. VIRTUO™ exhibited a faster TTD by an average of 3.5 h, as well as demonstrated a significantly improved detection rate of 99.9% compared to 98.8% with 3D (p-value <0.05).

Removal of Listeria monocytogenes dual-species biofilms using combined enzyme-benzalkonium chloride treatments.

PubMed

Rodríguez-López, Pedro; Carballo-Justo, Alba; Draper, Lorraine A; Cabo, Marta L

2017-01-01

The effects of pronase (PRN), cellulase (CEL) or DNaseI alone or combined with benzalkonium chloride (BAC) against Listeria monocytogenes-carrying biofilms were assayed. The best removal activity against L. monocytogenes-Escherichia coli biofilms was obtained using DNaseI followed by PRN and CEL. Subsequently, a modified logistic model was used to quantify the combined effects of PRN or DNaseI with BAC. A better BAC performance after PRN compared to DNaseI eradicating L. monocytogenes was observed. In E. coli the effects were the opposite. Finally, effects of DNaseI and DNaseI-BAC treatments were compared against two different L. monocytogenes-carrying biofilms. DNaseI-BAC was more effective against L. monocytogenes when co-cultured with E. coli. Nonetheless, comparing the removal effects after BAC addition, these were higher in mixed-biofilms with Pseudomonas fluorescens. However, a high number of released viable cells was observed after combined treatments. These results open new perspectives of enzymes as an anti-biofilm strategy for environmental pathogen control.

High-resolution mapping of genotype-phenotype relationships in cridu chat syndrome using array comparative genomic hybridization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard

2007-07-03

We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology tomore » 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.« less

Long-term exposure to benzalkonium chloride disinfectants results in change of microbial community structure and increased antimicrobial resistance.

PubMed

Tandukar, Madan; Oh, Seungdae; Tezel, Ulas; Konstantinidis, Konstantinos T; Pavlostathis, Spyros G

2013-09-03

The effect of benzalkonium chlorides (BACs), a widely used class of quaternary ammonium disinfectants, on microbial community structure and antimicrobial resistance was investigated using three aerobic microbial communities: BACs-unexposed (DP, fed a mixture of dextrin/peptone), BACs-exposed (DPB, fed a mixture of dextrin/peptone and BACs), and BACs-enriched (B, fed only BACs). Long-term exposure to BACs reduced community diversity and resulted in the enrichment of BAC-resistant species, predominantly Pseudomonas species. Exposure of the two microbial communities to BACs significantly decreased their susceptibility to BACs as well as three clinically relevant antibiotics (penicillin G, tetracycline, ciprofloxacin). Increased resistance to BACs and penicillin G of the two BACs-exposed communities is predominantly attributed to degradation or transformation of these compounds, whereas resistance to tetracycline and ciprofloxacin is largely due to the activity of efflux pumps. Quantification of several key multidrug resistance genes showed a much higher number of copies of these genes in the DPB and B microbial communities compared to the DP community. Collectively, our findings indicate that exposure of a microbial community to BACs results in increased antibiotic resistance, which has important implications for both human and environmental health.

Cloning of the Koi Herpesvirus Genome as an Infectious Bacterial Artificial Chromosome Demonstrates That Disruption of the Thymidine Kinase Locus Induces Partial Attenuation in Cyprinus carpio koi▿

PubMed Central

Costes, B.; Fournier, G.; Michel, B.; Delforge, C.; Raj, V. Stalin; Dewals, B.; Gillet, L.; Drion, P.; Body, A.; Schynts, F.; Lieffrig, F.; Vanderplasschen, A.

2008-01-01

Koi herpesvirus (KHV) is the causative agent of a lethal disease in koi and common carp. In the present study, we describe the cloning of the KHV genome as a stable and infectious bacterial artificial chromosome (BAC) clone that can be used to produce KHV recombinant strains. This goal was achieved by the insertion of a loxP-flanked BAC cassette into the thymidine kinase (TK) locus. This insertion led to a BAC plasmid that was stably maintained in bacteria and was able to regenerate virions when permissive cells were transfected with the plasmid. Reconstituted virions free of the BAC cassette but carrying a disrupted TK locus (the FL BAC-excised strain) were produced by the transfection of Cre recombinase-expressing cells with the BAC. Similarly, virions with a wild-type revertant TK sequence (the FL BAC revertant strain) were produced by the cotransfection of cells with the BAC and a DNA fragment encoding the wild-type TK sequence. Reconstituted recombinant viruses were compared to the wild-type parental virus in vitro and in vivo. The FL BAC revertant strain and the FL BAC-excised strain replicated comparably to the parental FL strain. The FL BAC revertant strain induced KHV infection in koi carp that was indistinguishable from that induced by the parental strain, while the FL BAC-excised strain exhibited a partially attenuated phenotype. Finally, the usefulness of the KHV BAC for recombination studies was demonstrated by the production of an ORF16-deleted strain by using prokaryotic recombination technology. The availability of the KHV BAC is an important advance that will allow the study of viral genes involved in KHV pathogenesis, as well as the production of attenuated recombinant candidate vaccines. PMID:18337580

Impact of ozonation and biological activated carbon filtration on ceramic membrane fouling.

PubMed

Ibn Abdul Hamid, Khaled; Sanciolo, Peter; Gray, Stephen; Duke, Mikel; Muthukumaran, Shobha

2017-12-01

Ozone pre-treatment (ozonation, ozonisation) and biological activated carbon (BAC) filtration pre-treatment for the ceramic microfiltration (CMF) treatment of secondary effluent (SE) were studied. Ozone pre-treatment was found to result in higher overall removal of UV absorbance (UVA 254 ) and colour, and higher permeability than BAC pre-treatment or the combined use of ozone and BAC (O3+BAC) pre-treatment. The overall removal of colour and UVA 254 by ceramic filtration of the ozone pre-treated water was 97% and 63% respectively, compared to 86% and 48% respectively for BAC pre-treatment and 29% and 6% respectively for the untreated water. Ozone pre-treatment, however, was not effective in removal of dissolved organic carbon (DOC). The permeability of the ozone pre-treated water through the ceramic membrane was found to decrease to 50% of the original value after 200 min of operation, compared to approximately 10% of the original value for the BAC pre-treated, O3+BAC pre-treated water and the untreated water. The higher permeability of the ozone pre-treated water was attributed to the excellent removal of biopolymer particles (100%) and high removal of humic substances (84%). The inclusion of a BAC stage between ozone pre-treatment and ceramic filtration was detrimental. The O3+BAC+CMF process was found to yield higher biopolymer removal (96%), lower humic substance (HS) component removal (66%) and lower normalized permeability (0.1) after 200 min of operation than the O3+CMF process (86%, 84% and 0.5 respectively). This was tentatively attributed to the chemical oxidation effect of ozone on the BAC biofilm and adsorbed components, leading to the generation of foulants that are not generated in the O3+CMF process. This study demonstrated the potential of ozone pre-treatment for reducing organic fouling and thus improving flux for the CMF of SE compared to O3+BAC pre-treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of the cytotoxic effects of ophthalmic solutions containing benzalkonium chloride on corneal epithelium using an organotypic 3-D model

PubMed Central

Khoh-Reiter, Su; Jessen, Bart A

2009-01-01

Background Benzalkonium chloride (BAC) is a common preservative used in ophthalmic solutions. The aim of this study was to compare the cytotoxic effects of BAC-containing ophthalmic solutions with a BAC-free ophthalmic solution using an organotypic 3-dimensional (3-D) corneal epithelial model and to determine the effects of latanoprost ophthalmic solution and its BAC-containing vehicle on corneal thickness in a monkey model. Methods The cytotoxicity of commercially available BAC-containing ophthalmic formulations of latanoprost (0.02% BAC) and olopatadine (0.01% BAC) was compared to that of BAC-free travoprost and saline in a corneal organotypic 3-D model using incubation times of 10 and 25 minutes. To compare the extent of differentiation of 3-D corneal cultures to monolayer transformed human corneal epithelial (HCE-T) cell cultures, expression levels (mRNA and protein) of the corneal markers epidermal growth factor receptor, transglutaminase 1 and involucrin were quantified. Finally, latanoprost ophthalmic solution or its vehicle was administered at suprapharmacologic doses (two 30 μL drops twice daily in 1 eye for 1 year) in monkey eyes, and corneal pachymetry was performed at baseline and at weeks 4, 13, 26 and 52. Results In the 3-D corneal epithelial culture assays, there were no significant differences in cytotoxicity between the BAC-containing latanoprost and olopatadine ophthalmic solutions and BAC-free travoprost ophthalmic solution at either the 10- or 25-minute time points. The 3-D cultures expressed higher levels of corneal epithelial markers than the HCE-T monolayers, indicating a greater degree of differentiation. There were no significant differences between the corneal thickness of monkey eyes treated with latanoprost ophthalmic solution or its vehicle (both containing 0.02% BAC) and untreated eyes. Conclusion The lack of cytotoxicity demonstrated in 3-D corneal cultures and in monkey studies suggests that the levels of BAC contained in ophthalmic solutions are not likely to cause significant direct toxicity to epithelium of otherwise normal corneas. PMID:19638217

X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation

PubMed Central

Madrigal, I; Rodríguez-Revenga, L; Armengol, L; González, E; Rodriguez, B; Badenas, C; Sánchez, A; Martínez, F; Guitart, M; Fernández, I; Arranz, JA; Tejada, MI; Pérez-Jurado, LA; Estivill, X; Milà, M

2007-01-01

Background Aproximately 5–10% of cases of mental retardation in males are due to copy number variations (CNV) on the X chromosome. Novel technologies, such as array comparative genomic hybridization (aCGH), may help to uncover cryptic rearrangements in X-linked mental retardation (XLMR) patients. We have constructed an X-chromosome tiling path array using bacterial artificial chromosomes (BACs) and validated it using samples with cytogenetically defined copy number changes. We have studied 54 patients with idiopathic mental retardation and 20 controls subjects. Results Known genomic aberrations were reliably detected on the array and eight novel submicroscopic imbalances, likely causative for the mental retardation (MR) phenotype, were detected. Putatively pathogenic rearrangements included three deletions and five duplications (ranging between 82 kb to one Mb), all but two affecting genes previously known to be responsible for XLMR. Additionally, we describe different CNV regions with significant different frequencies in XLMR and control subjects (44% vs. 20%). Conclusion This tiling path array of the human X chromosome has proven successful for the detection and characterization of known rearrangements and novel CNVs in XLMR patients. PMID:18047645

Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer

PubMed Central

Han, Wonshik; Han, Mi-Ryung; Kang, Jason Jongho; Bae, Ji-Yeon; Lee, Ji Hyun; Bae, Young Ju; Lee, Jeong Eon; Shin, Hyuk-Jae; Hwang, Ki-Tae; Hwang, Sung-Eun; Kim, Sung-Won; Noh, Dong-Young

2006-01-01

Background A considerable proportion of estrogen receptor (ER)-positive breast cancer recurs despite tamoxifen treatment, which is a serious problem commonly encountered in clinical practice. We tried to find novel prognostic markers in this subtype of breast cancer. Methods We performed array comparative genomic hybridization (CGH) with 1,440 human bacterial artificial chromosome (BAC) clones to assess copy number changes in 28 fresh-frozen ER-positive breast cancer tissues. All of the patients included had received at least 1 year of tamoxifen treatment. Nine patients had distant recurrence within 5 years (Recurrence group) of diagnosis and 19 patients were alive without disease at least 5 years after diagnosis (Non-recurrence group). Results Potential prognostic variables were comparable between the two groups. In an unsupervised clustering analysis, samples from each group were well separated. The most common regions of gain in all samples were 1q32.1, 17q23.3, 8q24.11, 17q12-q21.1, and 8p11.21, and the most common regions of loss were 6q14.1-q16.3, 11q21-q24.3, and 13q13.2-q14.3, as called by CGH-Explorer software. The average frequency of copy number changes was similar between the two groups. The most significant chromosomal alterations found more often in the Recurrence group using two different statistical methods were loss of 11p15.5-p15.4, 1p36.33, 11q13.1, and 11p11.2 (adjusted p values <0.001). In subgroup analysis according to lymph node status, loss of 11p15 and 1p36 were found more often in Recurrence group with borderline significance within the lymph node positive patients (adjusted p = 0.052). Conclusion Our array CGH analysis with BAC clones could detect various genomic alterations in ER-positive breast cancers, and Recurrence group samples showed a significantly different pattern of DNA copy number changes than did Non-recurrence group samples. PMID:16608533

Evaluation of the 3D BacT/ALERT automated culture system for the detection of microbial contamination of platelet concentrates.

PubMed

McDonald, C P; Rogers, A; Cox, M; Smith, R; Roy, A; Robbins, S; Hartley, S; Barbara, J A J; Rothenberg, S; Stutzman, L; Widders, G

2002-10-01

Bacterial transmission remains the major component of morbidity and mortality associated with transfusion-transmitted infections. Platelet concentrates are the most common cause of bacterial transmission. The BacT/ALERT 3D automated blood culture system has the potential to screen platelet concentrates for the presence of bacteria. Evaluation of this system was performed by spiking day 2 apheresis platelet units with individual bacterial isolates at final concentrations of 10 and 100 colony-forming units (cfu) mL-1. Fifteen organisms were used which had been cited in platelet transmission and monitoring studies. BacT/ALERT times to detection were compared with thioglycollate broth cultures, and the performance of five types of BacT/ALERT culture bottles was evaluated. Sampling was performed immediately after the inoculation of the units, and 10 replicates were performed per organism concentration for each of the five types of BacT/ALERT bottles. The mean times for the detection of these 15 organisms by BacT/ALERT, with the exception of Propionibacterium acnes, ranged from 9.1 to 48.1 h (all 10 replicates were positive). In comparison, the time range found using thioglycollate was 12.0-32.3 h (all 10 replicates were positive). P. acnes' BacT/ALERT mean detection times ranged from 89.0 to 177.6 h compared with 75.6-86.4 h for the thioglycollate broth. BacT/ALERT, with the exception of P. acnes, which has dubious clinical significance, gave equivalent or shorter detection times when compared with the thioglycollate broth system. The BacT/ALERT system detected a range of organisms at levels of 10 and 100 cfu mL-1. This study validates the BacT/ALERT microbial detection system for screening platelets. Currently, the system is the only practically viable option available for routinely screening platelet concentrates to prevent bacterial transmission.

A piggyBac-based reporter system for scalable in vitro and in vivo analysis of 3′ untranslated region-mediated gene regulation

PubMed Central

Chaudhury, Arindam; Kongchan, Natee; Gengler, Jon P.; Mohanty, Vakul; Christiansen, Audrey E.; Fachini, Joseph M.; Martin, James F.; Neilson, Joel R.

2014-01-01

Regulation of messenger ribonucleic acid (mRNA) subcellular localization, stability and translation is a central aspect of gene expression. Much of this control is mediated via recognition of mRNA 3′ untranslated regions (UTRs) by microRNAs (miRNAs) and RNA-binding proteins. The gold standard approach to assess the regulation imparted by a transcript's 3′ UTR is to fuse the UTR to a reporter coding sequence and assess the relative expression of this reporter as compared to a control. Yet, transient transfection approaches or the use of highly active viral promoter elements may overwhelm a cell's post-transcriptional regulatory machinery in this context. To circumvent this issue, we have developed and validated a novel, scalable piggyBac-based vector for analysis of 3′ UTR-mediated regulation in vitro and in vivo. The vector delivers three independent transcription units to the target genome—a selection cassette, a turboGFP control reporter and an experimental reporter expressed under the control of a 3′ UTR of interest. The pBUTR (piggyBac-based 3′ UnTranslated Region reporter) vector performs robustly as a siRNA/miRNA sensor, in established in vitro models of post-transcriptional regulation, and in both arrayed and pooled screening approaches. The vector is robustly expressed as a transgene during murine embryogenesis, highlighting its potential usefulness for revealing post-transcriptional regulation in an in vivo setting. PMID:24753411

Integrated in silico and biological validation of the blocking effect of Cot-1 DNA on Microarray-CGH.

PubMed

Kang, Seung-Hui; Park, Chan Hee; Jeung, Hei Cheul; Kim, Ki-Yeol; Rha, Sun Young; Chung, Hyun Cheol

2007-06-01

In array-CGH, various factors may act as variables influencing the result of experiments. Among them, Cot-1 DNA, which has been used as a repetitive sequence-blocking agent, may become an artifact-inducing factor in BAC array-CGH. To identify the effect of Cot-1 DNA on Microarray-CGH experiments, Cot-1 DNA was labeled directly and Microarray-CGH experiments were performed. The results confirmed that probes which hybridized more completely with Cot-1 DNA had a higher sequence similarity to the Alu element. Further, in the sex-mismatched Microarray-CGH experiments, the variation and intensity in the fluorescent signal were reduced in the high intensity probe group in which probes were better hybridized with Cot-1 DNA. Otherwise, those of the low intensity probe group showed no alterations regardless of Cot-1 DNA. These results confirmed by in silico methods that Cot-1 DNA could block repetitive sequences in gDNA and probes. In addition, it was confirmed biologically that the blocking effect of Cot-1 DNA could be presented via its repetitive sequences, especially Alu elements. Thus, in contrast to BAC-array CGH, the use of Cot-1 DNA is advantageous in controlling experimental variation in Microarray-CGH.

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

PubMed Central

Griffin, Darren K; Robertson, Lindsay B; Tempest, Helen G; Vignal, Alain; Fillon, Valérie; Crooijmans, Richard PMA; Groenen, Martien AM; Deryusheva, Svetlana; Gaginskaya, Elena; Carré, Wilfrid; Waddington, David; Talbot, Richard; Völker, Martin; Masabanda, Julio S; Burt, Dave W

2008-01-01

Background Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds. Results We present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs. Conclusion This is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents. PMID:18410676

Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer.

PubMed

Wang, Chun Ming; Lo, Loong Chueng; Feng, Felicia; Gong, Ping; Li, Jian; Zhu, Ze Yuan; Lin, Grace; Yue, Gen Hua

2008-03-25

Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. We reported herein a bacterial artificial chromosome (BAC) library and the mapping of BAC clones to the linkage map. This BAC library consisted of 49,152 clones with an average insert size of 98 kb, representing 6.9-fold haploid genome coverage. Screening the library with 24 microsatellites and 15 ESTs/genes demonstrated that the library had good genome coverage. In addition, 62 novel microsatellites each isolated from 62 BAC clones were mapped onto the first generation linkage map. A total of 86 BAC clones were anchored on the linkage map with at least one BAC clone on each linkage group. We have constructed the first BAC library for L. calcarifer and mapped 86 BAC clones to the first generation linkage map. This BAC library and the improved linkage map with 302 DNA markers not only supply an indispensable tool to the integration of physical and linkage maps, the fine mapping of QTL and map based cloning genes located in QTL of commercial importance, but also contribute to comparative genomic studies and eventually whole genome sequencing.

Baculovirus vectors expressing F proteins in combination with virus-induced signaling adaptor (VISA) molecules confer protection against respiratory syncytial virus infection.

PubMed

Zhang, Yuan; Qiao, Lei; Hu, Xiao; Zhao, Kang; Zhang, Yanwen; Chai, Feng; Pan, Zishu

2016-01-04

Baculovirus has been exploited for use as a novel vaccine vector. To investigate the feasibility and efficacy of recombinant baculoviruses (rBVs) expressing respiratory syncytial virus (RSV) fusion (F) proteins, four constructs (Bac-tF/64, Bac-CF, Bac-CF/tF64 and Bac-CF/tF64-VISA) were generated. Bac-tF64 displays the F ectodomain (tF) on the envelope of rBVs, whereas Bac-CF expresses full-length F protein in transduced mammalian cells. Bac-CF/tF64 not only displays tF on the envelope but also expresses F in cells. Bac-CF/tF64-VISA comprises Bac-CF/tF64 harboring the virus-induced signaling adaptor (VISA) gene. After administration to BALB/c mice, all four vectors elicited RSV neutralizing antibody (Ab), systemic Ab (IgG, IgG1, and IgG2a), and cytokine responses. Compared with Bac-tF64, mice inoculated with Bac-CF and Bac-CF/tF64 exhibited an increased mixed Th1/Th2 cytokine response, increased ratios of IgG2a/IgG1 antibody responses, and reduced immunopathology upon RSV challenge. Intriguingly, co-expression of VISA reduced Th2 cytokine (IL-4, IL-5, and IL-10) production induced by Bac-CF/tF64, thus relieving lung pathology upon a subsequent RSV challenge. Our results indicated that the Bac-CF/tF64 vector incorporated with the VISA molecule may provide an effective vaccine strategy for protection against RSV. Copyright © 2015 Elsevier Ltd. All rights reserved.

A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb

PubMed Central

2012-01-01

Background The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of ovine chromosome 20. The evolutionary consequence of such an inversion and an insertion (inversion/insertion) in relation to MHC function remains unknown. We previously constructed a BAC clone physical map for the ovine MHC exclusive of the insertion region. Here we report the construction of a high-density physical map covering the autosome insertion in order to address the question of what the inversion/insertion had to do with ruminants during the MHC evolution. Results A total of 119 pairs of comparative bovine oligo primers were utilized to screen an ovine BAC library for positive clones and the orders and overlapping relationships of the identified clones were determined by DNA fingerprinting, BAC-end sequencing, and sequence-specific PCR. A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb. Therefore, a continuous physical map covering the entire ovine autosome inversion/insertion region was successfully constructed. The map confirmed the bovine sequence assembly for the same homologous region. The DNA sequences of 185 BAC-ends have been deposited into NCBI database with the access numbers HR309252 through HR309068, corresponding to dbGSS ID 30164010 through 30163826. Conclusions We have constructed a high-density BAC clone physical map for the ovine autosome inversion/insertion between the MHC class IIa and IIb. The entire ovine MHC region is now fully covered by a continuous BAC clone contig. The physical map we generated will facilitate MHC functional studies in the ovine, as well as the comparative MHC evolution in ruminants. PMID:22897909

Time to Detection with BacT/Alert FA Plus Compared to BacT/Alert FA Blood Culture Media.

PubMed

Nutman, A; Fisher Even-Tsur, S; Shapiro, G; Braun, T; Schwartz, D; Carmeli, Y

2016-09-01

Rapid identification of the causative pathogen in patients with bacteremia allows adjustment of antibiotic therapy and improves patient outcomes. We compared in vitro and real-life time to detection (TTD) of two blood culture media, BacT/Alert FA (FA) and BacT/Alert FA Plus (FA Plus), for the nine most common species of bacterial pathogens recovered from blood samples. Experimental data from simulated cultures was compared with microbiology records of TTD for both culture media with growth of the species of interest in clinical blood cultures. In the experimental conditions, median TTD was 3.8 hours (23.9 %) shorter using FA Plus media. The magnitude of reduction differed between species. Similarly, in real life data, FA Plus had shorter TTD than FA media; however, the difference between culture media was smaller, and median TTD was only 1 hour (8.5 %) less. We found shorter TTD with BacT/Alert FA Plus culture media, both experimentally and in real-life conditions and unrelated to antibiotic neutralization, highlighting the importance of appropriate blood culture media selection.

In vitro antibacterial and cytotoxicity assessments of an orthodontic bonding agent containing benzalkonium chloride.

PubMed

Saito, Kayo; Hayakawa, Tohru; Kawabata, Rihito; Meguro, Daijiro; Kasai, Kazutaka

2009-03-01

To assess the antibacterial activity and cytotoxicity of an orthodontic bonding material containing an antibacterial agent. Superbond C&B (4-methacryloxyethyl trimellitate anhydride/methyl methacrylate-tri-n-butyl borane [4-META/MMA-TBB]) resin was mixed with benzalkonium chloride (BAC) to obtain final BAC concentrations of 0.25%, 0.75%, 1.25%, 1.75%, 2.5%, and 5.0% (wt/ wt). Antibacterial activity against Streptococcus mutans and Streptococcus sobrinus was evaluated by soaking the BAC-resin in distilled water at 37 degrees C for periods of 30, 90, and 180 days. Antibacterial activity of the BAC-resin was measured by the disk diffusion method, and the inhibition zone around each sample was measured and recorded. For evaluation of cytotoxicity, BAC-resin samples were put into cell culture inserts placed above human gingival cells and were incubated at 37 degrees C for 1, 3, and 6 days. Cytotoxicity was assessed with a tetrazolium bromide reduction assay. The antibacterial activity of BAC-incorporated resin samples decreased significantly after immersion in water for 180 days, regardless of BAC concentration. The antibacterial activity of nonimmersed resin containing 0.25% or 1.75% BAC was comparable with that of 5.0% BAC-resin immersed for 180 days. In cytotoxicity tests, most cells died when exposed to resins containing 1.75%, 2.5%, and 5% BAC. No difference was observed between resins containing 0.25% and 0.75% BAC at 1, 3, and 6 days of culture. The addition of BAC to 4-META/MMA-TBB resin confers an antibacterial effect even after immersion in water, and 4-META/MMA-TBB resin containing 0.25% to 0.75% BAC has no significant cytotoxic effect.

Research on the stability of a rabbit dry eye model induced by topical application of the preservative benzalkonium chloride.

PubMed

Li, Chaoyang; Song, Yiyue; Luan, Shaohong; Wan, Pengxia; Li, Naiyang; Tang, Jing; Han, Yu; Xiong, Cuiju; Wang, Zhichong

2012-01-01

Dry eye is a common disease worldwide, and animal models are critical for the study of it. At present, there is no research about the stability of the extant animal models, which may have negative implications for previous dry eye studies. In this study, we observed the stability of a rabbit dry eye model induced by the topical benzalkonium chloride (BAC) and determined the valid time of this model. Eighty white rabbits were randomly divided into four groups. One eye from each rabbit was randomly chosen to receive topical 0.1% BAC twice daily for 2 weeks (Group BAC-W2), 3 weeks (Group BAC-W3), 4 weeks (Group BAC-W4), or 5 weeks (Group BAC-W5). Fluorescein staining, Schirmer's tests, and conjunctival impression cytology were performed before BAC treatment (normal) and on days 0, 7, 14 and 21 after BAC removal. The eyeballs were collected at these time points for immunofluorescence staining, hematoxylin and eosin (HE) staining, and electron microscopy. After removing BAC, the signs of dry eye in Group BAC-W2 lasted one week. Compared with normal, there were still significant differences in the results of Schirmer's tests and fluorescein staining in Groups BAC-W3 and BAC-W4 on day 7 (P<0.05) and in Group BAC-W5 on day 14 (P<0.05). Decreases in goblet cell density remained stable in the three experimental groups at all time points (P<0.001). Decreased levels of mucin-5 subtype AC (MUC5AC), along with histopathological and ultrastructural disorders of the cornea and conjunctiva could be observed in Group BAC-W4 and particularly in Group BAC-W5 until day 21. A stable rabbit dry eye model was induced by topical 0.1% BAC for 5 weeks, and after BAC removal, the signs of dry eye were sustained for 2 weeks (for the mixed type of dry eye) or for at least 3 weeks (for mucin-deficient dry eye).

Research on the Stability of a Rabbit Dry Eye Model Induced by Topical Application of the Preservative Benzalkonium Chloride

PubMed Central

Luan, Shaohong; Wan, Pengxia; Li, Naiyang; Tang, Jing; Han, Yu; Xiong, Cuiju; Wang, Zhichong

2012-01-01

Background Dry eye is a common disease worldwide, and animal models are critical for the study of it. At present, there is no research about the stability of the extant animal models, which may have negative implications for previous dry eye studies. In this study, we observed the stability of a rabbit dry eye model induced by the topical benzalkonium chloride (BAC) and determined the valid time of this model. Methods and Findings Eighty white rabbits were randomly divided into four groups. One eye from each rabbit was randomly chosen to receive topical 0.1% BAC twice daily for 2 weeks (Group BAC-W2), 3 weeks (Group BAC-W3), 4 weeks (Group BAC-W4), or 5 weeks (Group BAC-W5). Fluorescein staining, Schirmer's tests, and conjunctival impression cytology were performed before BAC treatment (normal) and on days 0, 7, 14 and 21 after BAC removal. The eyeballs were collected at these time points for immunofluorescence staining, hematoxylin and eosin (HE) staining, and electron microscopy. After removing BAC, the signs of dry eye in Group BAC-W2 lasted one week. Compared with normal, there were still significant differences in the results of Schirmer's tests and fluorescein staining in Groups BAC-W3 and BAC-W4 on day 7 (P<0.05) and in Group BAC-W5 on day 14 (P<0.05). Decreases in goblet cell density remained stable in the three experimental groups at all time points (P<0.001). Decreased levels of mucin-5 subtype AC (MUC5AC), along with histopathological and ultrastructural disorders of the cornea and conjunctiva could be observed in Group BAC-W4 and particularly in Group BAC-W5 until day 21. Conclusions A stable rabbit dry eye model was induced by topical 0.1% BAC for 5 weeks, and after BAC removal, the signs of dry eye were sustained for 2 weeks (for the mixed type of dry eye) or for at least 3 weeks (for mucin-deficient dry eye). PMID:22438984

The combined rapid detection and species-level identification of yeasts in simulated blood culture using a colorimetric sensor array

PubMed Central

Lim, Sung H.; Wilson, Deborah A.; SalasVargas, Ana Victoria; Churi, Yair S.; Rhodes, Paul A.; Mazzone, Peter J.; Procop, Gary W.

2017-01-01

Background A colorimetric sensor array (CSA) has been demonstrated to rapidly detect and identify bacteria growing in blood cultures by obtaining a species-specific “fingerprint” of the volatile organic compounds (VOCs) produced during growth. This capability has been demonstrated in prokaryotes, but has not been reported for eukaryotic cells growing in culture. The purpose of this study was to explore if a disposable CSA could differentially identify 7 species of pathogenic yeasts growing in blood culture. Methods Culture trials of whole blood inoculated with a panel of clinically important pathogenic yeasts at four different microorganism loads were performed. Cultures were done in both standard BacT/Alert and CSA-embedded bottles, after adding 10 mL of spiked blood to each bottle. Color changes in the CSA were captured as images by an optical scanner at defined time intervals. The captured images were analyzed to identify the yeast species. Time to detection by the CSA was compared to that in the BacT/Alert system. Results One hundred sixty-two yeast culture trials were performed, including strains of several species of Candida (Ca. albicans, Ca. glabrata, Ca. parapsilosis, and Ca. tropicalis), Clavispora (synonym Candida) lusitaniae, Pichia kudriavzevii (synonym Candida krusei) and Cryptococcus neoformans, at loads of 8.2 × 105, 8.3 × 103, 8.5 × 101, and 1.7 CFU/mL. In addition, 8 negative trials (no yeast) were conducted. All negative trials were correctly identified as negative, and all positive trials were detected. Colorimetric responses were species-specific and did not vary by inoculum load over the 500000-fold range of loads tested, allowing for accurate species-level identification. The mean sensitivity for species-level identification by CSA was 74% at detection, and increased with time, reaching almost 95% at 4 hours after detection. At an inoculum load of 1.7 CFU/mL, mean time to detection with the CSA was 6.8 hours (17%) less than with the BacT/Alert platform. Conclusion The CSA combined rapid detection of pathogenic yeasts in blood culture with accurate species-level identification. PMID:28296967

The combined rapid detection and species-level identification of yeasts in simulated blood culture using a colorimetric sensor array.

PubMed

Shrestha, Nabin K; Lim, Sung H; Wilson, Deborah A; SalasVargas, Ana Victoria; Churi, Yair S; Rhodes, Paul A; Mazzone, Peter J; Procop, Gary W

2017-01-01

A colorimetric sensor array (CSA) has been demonstrated to rapidly detect and identify bacteria growing in blood cultures by obtaining a species-specific "fingerprint" of the volatile organic compounds (VOCs) produced during growth. This capability has been demonstrated in prokaryotes, but has not been reported for eukaryotic cells growing in culture. The purpose of this study was to explore if a disposable CSA could differentially identify 7 species of pathogenic yeasts growing in blood culture. Culture trials of whole blood inoculated with a panel of clinically important pathogenic yeasts at four different microorganism loads were performed. Cultures were done in both standard BacT/Alert and CSA-embedded bottles, after adding 10 mL of spiked blood to each bottle. Color changes in the CSA were captured as images by an optical scanner at defined time intervals. The captured images were analyzed to identify the yeast species. Time to detection by the CSA was compared to that in the BacT/Alert system. One hundred sixty-two yeast culture trials were performed, including strains of several species of Candida (Ca. albicans, Ca. glabrata, Ca. parapsilosis, and Ca. tropicalis), Clavispora (synonym Candida) lusitaniae, Pichia kudriavzevii (synonym Candida krusei) and Cryptococcus neoformans, at loads of 8.2 × 105, 8.3 × 103, 8.5 × 101, and 1.7 CFU/mL. In addition, 8 negative trials (no yeast) were conducted. All negative trials were correctly identified as negative, and all positive trials were detected. Colorimetric responses were species-specific and did not vary by inoculum load over the 500000-fold range of loads tested, allowing for accurate species-level identification. The mean sensitivity for species-level identification by CSA was 74% at detection, and increased with time, reaching almost 95% at 4 hours after detection. At an inoculum load of 1.7 CFU/mL, mean time to detection with the CSA was 6.8 hours (17%) less than with the BacT/Alert platform. The CSA combined rapid detection of pathogenic yeasts in blood culture with accurate species-level identification.

The effects of alcohol mixed with energy drink (AMED) on subjective intoxication and alertness: results from a double-blind placebo-controlled clinical trial.

PubMed

van de Loo, Aurora J A E; van Andel, Nienke; van Gelder, Charlotte A G H; Janssen, Boris S G; Titulaer, Joep; Jansen, Jimmy; Verster, Joris C

2016-05-01

The purpose of this double blind placebo controlled study was to examine if specific effects on subjective intoxication and alertness-sleepiness ratings could be demonstrated after consuming alcohol mixed with energy drink (AMED) when compared to consuming alcohol only (AO). 56 healthy volunteers rated their subjective intoxication on a scale ranging from 0 (sober) to 10 (highly intoxicated) at baseline, breath alcohol concentration (BAC) of 0%, and at BAC 0.08%, 0.05%, and 0.02%. Alertness-sleepiness was assessed with the Karolinska sleepiness scale. Scores of the AMED and AO condition, at each BAC level, were compared. Subjective intoxication for AMED and AO did not differ significantly from each other at any BAC level, except for BAC 0.02%. A significant increase in sleepiness scores was found in the AO condition, whereas scores remained stable in the AMED condition. Sleepiness scores at BAC0.08% and 0.05% were significantly lower after AMED when compared to AO. However, the observed differences between AMED and AO were small and have no clinical relevance. Mixing alcohol with energy drink had no overall masking effect on subjective intoxication caused by alcohol, nor had a relevant effect on subjective alertness-sleepiness ratings. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant

PubMed Central

Hannes, F D; Sharp, A J; Mefford, H C; de Ravel, T; Ruivenkamp, C A; Breuning, M H; Fryns, J-P; Devriendt, K; Van Buggenhout, G; Vogels, A; Stewart, H; Hennekam, R C; Cooper, G M; Regan, R; Knight, S J L; Eichler, E E; Vermeesch, J R

2009-01-01

Background: Genomic disorders are often caused by non-allelic homologous recombination between segmental duplications. Chromosome 16 is especially rich in a chromosome-specific low copy repeat, termed LCR16. Methods and Results: A bacterial artificial chromosome (BAC) array comparative genome hybridisation (CGH) screen of 1027 patients with mental retardation and/or multiple congenital anomalies (MR/MCA) was performed. The BAC array CGH screen identified five patients with deletions and five with apparently reciprocal duplications of 16p13 covering 1.65 Mb, including 15 RefSeq genes. In addition, three atypical rearrangements overlapping or flanking this region were found. Fine mapping by high-resolution oligonucleotide arrays suggests that these deletions and duplications result from non-allelic homologous recombination (NAHR) between distinct LCR16 subunits with >99% sequence identity. Deletions and duplications were either de novo or inherited from unaffected parents. To determine whether these imbalances are associated with the MR/MCA phenotype or whether they might be benign variants, a population of 2014 normal controls was screened. The absence of deletions in the control population showed that 16p13.11 deletions are significantly associated with MR/MCA (p = 0.0048). Despite phenotypic variability, common features were identified: three patients with deletions presented with MR, microcephaly and epilepsy (two of these had also short stature), and two other deletion carriers ascertained prenatally presented with cleft lip and midline defects. In contrast to its previous association with autism, the duplication seems to be a common variant in the population (5/1682, 0.29%). Conclusion: These findings indicate that deletions inherited from clinically normal parents are likely to be causal for the patients’ phenotype whereas the role of duplications (de novo or inherited) in the phenotype remains uncertain. This difference in knowledge regarding the clinical relevance of the deletion and the duplication causes a paradigm shift in (cyto)genetic counselling. PMID:18550696

Construction of an infectious clone of canine herpesvirus genome as a bacterial artificial chromosome.

PubMed

Arii, Jun; Hushur, Orkash; Kato, Kentaro; Kawaguchi, Yasushi; Tohya, Yukinobu; Akashi, Hiroomi

2006-04-01

Canine herpesvirus (CHV) is an attractive candidate not only for use as a recombinant vaccine to protect dogs from a variety of canine pathogens but also as a viral vector for gene therapy in domestic animals. However, developments in this area have been impeded by the complicated techniques used for eukaryotic homologous recombination. To overcome these problems, we used bacterial artificial chromosomes (BACs) to generate infectious BACs. Our findings may be summarized as follows: (i) the CHV genome (pCHV/BAC), in which a BAC flanked by loxP sites was inserted into the thymidine kinase gene, was maintained in Escherichia coli; (ii) transfection of pCHV/BAC into A-72 cells resulted in the production of infectious virus; (iii) the BAC vector sequence was almost perfectly excisable from the genome of the reconstituted virus CHV/BAC by co-infection with CHV/BAC and a recombinant adenovirus that expressed the Cre recombinase; and (iv) a recombinant virus in which the glycoprotein C gene was deleted was generated by lambda recombination followed by Flp recombination, which resulted in a reduction in viral titer compared with that of the wild-type virus. The infectious clone pCHV/BAC is useful for the modification of the CHV genome using bacterial genetics, and CHV/BAC should have multiple applications in the rapid generation of genetically engineered CHV recombinants and the development of CHV vectors for vaccination and gene therapy in domestic animals.

Prolonged exposure of mixed aerobic cultures to low temperature and benzalkonium chloride affect the rate and extent of nitrification.

PubMed

Yang, Jeongwoo; Tezel, Ulas; Li, Kexun; Pavlostathis, Spyros G

2015-03-01

The combined effect of benzalkonium chloride (BAC) and prolonged exposure to low temperature on nitrification was investigated. Ammonia oxidation at 22-24°C by an enriched nitrifying culture was inhibited at increasing BAC concentrations and ceased at 15 mg BAC/L. The non-competitive inhibition coefficient was 1.5±0.9 mg BAC/L. Nitrification tests were conducted without and with BAC at 5mg/L using an aerobic, mixed heterotrophic/nitrifying culture maintained at a temperature range of 24-10°C. Maintaining this culture at 10°C for over one month in the absence of BAC, resulted in slower nitrification kinetics compared to those measured when the culture was first exposed to 10°C. BAC was degraded by the heterotrophic population, but its degradation rate decreased significantly as the culture temperature decreased to 10°C. These results confirm the negative impact of quaternary ammonium compounds on the nitrification process, which is further exacerbated by prolonged, low temperature conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes

PubMed Central

2011-01-01

Background A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. Results The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes. Conclusion The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species. PMID:21906286

A comparison of the effect of mobile phone use and alcohol consumption on driving simulation performance.

PubMed

Leung, Sumie; Croft, Rodney J; Jackson, Melinda L; Howard, Mark E; McKenzie, Raymond J

2012-01-01

The present study compared the effects of a variety of mobile phone usage conditions to different levels of alcohol intoxication on simulated driving performance and psychomotor vigilance. Twelve healthy volunteers participated in a crossover design in which each participant completed a simulated driving task on 2 days, separated by a 1-week washout period. On the mobile phone day, participants performed the simulated driving task under each of 4 conditions: no phone usage, a hands-free naturalistic conversation, a hands-free cognitively demanding conversation, and texting. On the alcohol day, participants performed the simulated driving task at four different blood alcohol concentration (BAC) levels: 0.00, 0.04, 0.07, and 0.10. Driving performance was assessed by variables including time within target speed range, time spent speeding, braking reaction time, speed deviation, and lateral lane position deviation. In the BAC 0.07 and 0.10 alcohol conditions, participants spent less time in the target speed range and more time speeding and took longer to brake in the BAC 0.04, 0.07, and 0.10 than in the BAC 0.00 condition. In the mobile phone condition, participants took longer to brake in the natural hands-free conversation, cognitively demanding hands-free conversation and texting conditions and spent less time in the target speed range and more time speeding in the cognitively demanding, hands-free conversation, and texting conditions. When comparing the 2 conditions, the naturalistic conversation was comparable to the legally permissible BAC level (0.04), and the cognitively demanding and texting conversations were similar to the BAC 0.07 to 0.10 results. The findings of the current laboratory study suggest that very simple conversations on a mobile phone may not represent a significant driving risk (compared to legally permissible BAC levels), whereas cognitively demanding, hands-free conversation, and particularly texting represent significant risks to driving.

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca).

PubMed

Zheng, Yang; Cai, Jing; Li, JianWen; Li, Bo; Lin, Runmao; Tian, Feng; Wang, XiaoLing; Wang, Jun

2010-01-01

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

Tolerance development in Listeria monocytogenes-Escherichia coli dual-species biofilms after sublethal exposures to pronase-benzalkonium chloride combined treatments.

PubMed

Rodríguez-López, Pedro; Cabo, Marta López

2017-10-01

This study was designed to assess the effects that sublethal exposures to pronase (PRN) and benzalkonium chloride (BAC) combined treatments have on Listeria monocytogenes-Escherichia coli dual-species biofilms grown on stainless steel in terms of tolerance development (TD) to these compounds. Additionally, fluorescence microscopy was used to observe the changes of the biofilm structure. PRN-BAC exposure was carried out using three different approaches and TD was evaluated treating biofilms with a final 100 μg/ml PRN followed by 50 μg/ml BAC combined treatment. Results showed that exposure to PRN-BAC significantly decreased the number of adhered L. monocytogenes (P < 0.05), while E. coli counts remained generally unaltered. It was also demonstrated that the incorporation of recovery periods during sublethal exposures increased the tolerance of both species of the mixed biofilm to the final PRN-BAC treatment. Moreover, control biofilms became more resistant to PRN-BAC if longer incubation periods were used. Regardless of the treatment used, log reduction values were generally lower in L. monocytogenes compared to E. coli. Additionally, microscopy images showed an altered morphology produced by sublethal PRN-BAC in exposed L. monocytogenes-E. coli dual-species biofilms compared to control samples. Results also demonstrated that L. monocytogenes-E. coli dual-species biofilms are able to develop tolerance to PRN-BAC combined treatments depending on way they have been previously exposed. Moreover, they suggest that the generation of bacterial tolerance should be included as a parameter for sanitation procedures design. Copyright © 2017 Elsevier Ltd. All rights reserved.

Validation of the tablet-administered Brief Assessment of Cognition (BAC App).

PubMed

Atkins, Alexandra S; Tseng, Tina; Vaughan, Adam; Twamley, Elizabeth W; Harvey, Philip; Patterson, Thomas; Narasimhan, Meera; Keefe, Richard S E

2017-03-01

Computerized tests benefit from automated scoring procedures and standardized administration instructions. These methods can reduce the potential for rater error. However, especially in patients with severe mental illnesses, the equivalency of traditional and tablet-based tests cannot be assumed. The Brief Assessment of Cognition in Schizophrenia (BACS) is a pen-and-paper cognitive assessment tool that has been used in hundreds of research studies and clinical trials, and has normative data available for generating age- and gender-corrected standardized scores. A tablet-based version of the BACS called the BAC App has been developed. This study compared performance on the BACS and the BAC App in patients with schizophrenia and healthy controls. Test equivalency was assessed, and the applicability of paper-based normative data was evaluated. Results demonstrated the distributions of standardized composite scores for the tablet-based BAC App and the pen-and-paper BACS were indistinguishable, and the between-methods mean differences were not statistically significant. The discrimination between patients and controls was similarly robust. The between-methods correlations for individual measures in patients were r>0.70 for most subtests. When data from the Token Motor Test was omitted, the between-methods correlation of composite scores was r=0.88 (df=48; p<0.001) in healthy controls and r=0.89 (df=46; p<0.001) in patients, consistent with the test-retest reliability of each measure. Taken together, results indicate that the tablet-based BAC App generates results consistent with the traditional pen-and-paper BACS, and support the notion that the BAC App is appropriate for use in clinical trials and clinical practice. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Effect of intracolonic benzalkonium chloride on trinitrobenzene sulphonic acid-induced colitis in the rat.

PubMed

Miampamba, M; Parr, E J; McCafferty, D M; Wallace, J L; Sharkey, K A

1998-03-01

We investigated the effects of benzalkonium chloride (BAC) on trinitrobenzene sulphonic acid (TNBS)-induced colitis in rats. TNBS was administered intrarectally before and/or after BAC treatment. In the first study, the effects of treatment with BAC 6, 12 or 24 h after TNBS were examined. In the second study, animals were treated with BAC before, after or before and after TNBS, and were examined 7 days later. The severity of colitis was assessed by macroscopic and histological scoring of the colonic damage and by determination of colonic myeloperoxidase (MPO) activity. Macrophages and CD4+ and CD8+ T cells were examined by immunohistochemistry. When BAC was instilled into the colon 6, 12 or 24 h after TNBS, weight loss and macroscopic and histological features of the colon were similar to that of controls (TNBS alone). In contrast, MPO activity was significantly reduced in all three groups post-treated with BAC. In the groups examined 7 days after TNBS treatment, rats post-treated with BAC exhibited increased weight gain and significantly reduced macroscopic damage and MPO activity compared to the TNBS control group. Rats pre-treated with BAC exhibited less macroscopic damage of the colon than rats receiving only TNBS, but histological damage, MPO and weight gain were unchanged from TNBS controls. Immunohistochemistry revealed that BAC pre-treatment increased the numbers of macrophages and T cells in the colon. After TNBS treatment, macrophage accumulation was evident in the colon, but T cells were scarce. However, these cells were preserved or enhanced in the colonic mucosa in TNBS-treated rats that had been pre-treated with BAC. Treatment with BAC, particularly after induction of colitis, produces a significant reduction in the severity of tissue injury and inflammation through mechanisms that are not fully understood.

Role of epidermal growth factor receptor tyrosine kinase inhibitors in the treatment of bronchoalveolar carcinoma.

PubMed

Patel, Jyoti D

2004-12-01

Bronchoalveolar carcinoma (BAC) is a previously uncommon subset of non-small-cell lung cancer (NSCLC) with unique epidemiology, pathology, clinical features, and natural history compared with other NSCLC subtypes. Recent data indicate that the incidence of BAC is increasing. Although many studies have reported that patients with BAC have prolonged survival, advanced BAC remains incurable, with most patients eventually dying of respiratory failure from progressive pulmonary involvement or intercurrent illness. Previous limited data suggest that chemotherapy for BAC provides modest benefit; however, anecdotal reports of swift and durable responses after treatment with tyrosine kinase (TK) inhibitors of the epidermal growth factor receptor (EGFR) in patients with BAC have prompted further investigation in this subset of patients. Two trials using the EGFR TK inhibitors gefitinib and/or erlotinib have demonstrated encouraging results, and have prompted further enthusiasm for this approach. Furthermore, recent insights into mechanisms of drug sensitivity should impact future clinical trial design.

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

PubMed

Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2016-07-01

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Performance of Two Resin-Containing Blood Culture Media in Detection of Bloodstream Infections and in Direct Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS) Broth Assays for Isolate Identification: Clinical Comparison of the BacT/Alert Plus and Bactec Plus Systems

PubMed Central

Fiori, Barbara; D'Inzeo, Tiziana; Di Florio, Viviana; De Maio, Flavio; De Angelis, Giulia; Giaquinto, Alessia; Campana, Lara; Tanzarella, Eloisa; Tumbarello, Mario; Antonelli, Massimo; Spanu, Teresa

2014-01-01

We compared the clinical performances of the BacT/Alert Plus (bioMérieux) and Bactec Plus (Becton Dickinson) aerobic and anaerobic blood culture (BC) media with adsorbent polymeric beads. Patients ≥16 years old with suspected bloodstream infections (BSIs) were enrolled in intensive care units and infectious disease wards. A single 40-ml blood sample was collected from each and used to inoculate (10 ml/bottle) one set of BacT/Alert Plus cultures and one set of Bactec Plus cultures, each set consisting of one aerobic and one anaerobic bottle. Cultures were incubated ≤5 days in the BacT/Alert 3D and Bactec FX instruments, respectively. A total of 128 unique BSI episodes were identified based on the recovery of clinically significant growth in 212 aerobic cultures (106 BacT/Alert and 106 Bactec) and 151 anaerobic cultures (82 BacT/Alert and 69 Bactec). The BacT/Alert aerobic medium had higher recovery rates for Gram-positive cocci (P = 0.024), whereas the Bactec aerobic medium was superior for recovery of Gram-negative bacilli (P = 0.006). BacT/Alert anaerobic medium recovery rates exceeded those of the Bactec anaerobic medium for total organisms (P = 0.003), Gram-positive cocci (P = 0.013), and Escherichia coli (P = 0.030). In terms of capacity for diagnosing the 128 septic episodes, the BacT/Alert and Bactec sets were comparable, although the former sets diagnosed more BSIs caused by Gram-positive cocci (P = 0.008). They also allowed earlier identification of coagulase-negative staphylococcal growth (mean, 2.8 h; P = 0.003) and growth in samples from patients not on antimicrobial therapy that yielded positive results (mean, 1.3 h; P < 0.001). Similarly high percentages of microorganisms in BacT/Alert and Bactec cultures (93.8% and 93.3%, respectively) were identified by direct matrix-assisted laser desorption ionization–time of flight mass spectrometry assay of BC broths. The BacT/Alert Plus media line appears to be a reliable, timesaving tool for routine detection of BSIs in the population we studied, although further studies are needed to evaluate their performance in other settings. PMID:25031441

Application of EDTA-functionalized bamboo activated carbon (BAC) for Pb(II) and Cu(II) removal from aqueous solutions

NASA Astrophysics Data System (ADS)

Lv, Dan; Liu, Yu; Zhou, Jiasheng; Yang, Kunlun; Lou, Zimo; Baig, Shams Ali; Xu, Xinhua

2018-01-01

In this study, a novel bamboo activated carbon (BAC) with ethylene diamine tetraacetic acid (EDTA) functionality was prepared by direct grafting in the presence of tetraethyl orthosilicate (TEOS) as a crosslinking agent. The BAC@SiO2-EDTA was characterized by SEM, TEM, TGA, FTIR, XPS and its adsorption property for removal of Pb(II) and Cu(II) under various experimental conditions was also investigated. The characterization results reflected that EDTA was successfully assembled on the surface of the BAC and average pore size increased from 4.10 to 4.83 nm as BAC grafted with EDTA. Adsorption data fitted very well in Langmuir isotherm model and pseudo-second-order kinetic model. As compared with the raw BAC, the maximum adsorption capacities of BAC@SiO2-EDTA for the Pb(II) and Cu(II) increased from 45.45 to 123.45 mg g-1 and from 6.85 to 42.19 mg g-1, since the existence of EDTA on modified BAC promoted the formation of chemical complex. The removal of heavy metal ions mainly depended on the complexation with EDTA and the electrostatic attractions with negatively charged surface of BAC@SiO2-EDTA. The adsorption of Pb(II)/Cu(II) on the BAC@SiO2-EDTA was pH dependent and pH 5-6 was considered an optimum. However, lower temperature favored the adsorption and the maximum adsorption was recorded at 20 °C. In addition, BAC@SiO2-EDTA had an excellent reusability with about 40% decline in the adsorption capacity for Pb(II) after fifth reuse. Insignificant influences of co-existing cations and natural organic matter (NOM) were found on the adsorption of Pb(II) and Cu(II). All the results demonstrate that BAC@SiO2-EDTA is a potential adsorbent for metal ions in wastewater.

M25. Development and Validation of the Brief Assessment of Validation in Schizophrenia (BAC-App)

PubMed Central

Atkins, Alexandra; Tseng, Tina; Vaughan, Adam; Harvey, Philip; Narasimhan, Meera; Patterson, Tom; Khan, Anzalee; Keefe, Richard

2017-01-01

Abstract Background: The Brief Assessment of Cognition in Schizophrenia (BACS) is a pen-and-paper cognitive assessment tool that has been used in hundreds of research studies and clinical trials, and has normative data available for generating age- and gender-corrected standardized scores. A tablet-based version of the BACS called the BAC App has been developed to allow standardized presentation of task instructions and stimuli, audio-recording of subject responses, and automatized scoring and data management. Development of the BAC App was aimed at reducing rater burden and variability. Our validation study compared performance on the traditional BACS and the BAC App in patients with schizophrenia and healthy controls. Test equivalency was assessed, and the applicability of paper-based normative data was evaluated. An ongoing follow-up study examines BAC App performance in large-scale census-matched normative sample. Methods: Participants in the validation study included 48 patients (23 female) with schizophrenia and 50 healthy controls (25 female) recruited from 3 academic sites including the University of California-San Diego, the University of Miami—Miller School of Medicine, and the University of South Carolina. All participants were assessed with the standard pen-and-paper BACS and the BAC App. Ongoing normative evaluation of the BAC App will include a community sample of 650 individuals matched to the US census on age, education, race and gender. Results: In the validation study, distributions of standardized composite scores for the tablet-based BAC App and the pen-and-paper BACS were indistinguishable in both schizophrenia patients and healthy controls. Between-methods mean differences were not statistically significant. The discrimination between patients and controls was similarly robust with the BAC App (d = 1.34) and the BACS (d = 1.24). The between-methods correlations for individual measures in patients were r > .70 except Token Motor (r = .43) and Tower of London (r = .61). In patients, performance between the test methods was not significantly different on any test except the Token Motor Test. When data from the Token Motor Test were removed, the between-methods correlation of composite scores improved to r = .88 (df = 48; P <.001) in healthy controls and r = .89 (df = 46; P < .001) in patients, consistent with the test-retest reliability of each measure. Interim findings from the ongoing normative study (N = 52 to date) suggest that the BAC App is well-tolerated by a diverse community population, with 78.9% (N = 41) of subjects rating their experience with the BAC App as “pleasant” on a 7-point Likert scale. Conclusion: The tablet-based BAC App is generates results consistent with the traditional pen-and-paper BACS. These data support the notion that the BAC App can now be used in clinical trials and clinical practice.

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

PubMed Central

2011-01-01

Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of the zebrafish genome. BES of common carp are tremendous tools for comparative mapping between the two closely related species, zebrafish and common carp, which should facilitate both structural and functional genome analysis in common carp. PMID:21492448

Demographic and socioeconomic factors influencing disparities in prevalence of alcohol-related injury among underserved trauma patients in a safety-net hospital.

PubMed

Nweze, Ikenna C; DiGiacomo, Jody C; Shin, Silvia S; Gupta, Camilla; Ramakrishnan, Rema; Angus, Lambros D G

2016-12-01

Alcohol-related trauma remains high among underserved patients despite ongoing preventive measures. Geographic variability in prevalence of alcohol-related injury has prompted reexamination of this burden across different regions. We sought to elucidate demographic and socioeconomic factors influencing the prevalence of alcohol-related trauma among underserved patients and determine alcohol effects on selected outcomes. A retrospective analysis examined whether patients admitted to a suburban trauma center differed according to their blood alcohol concentration (BAC) on admission. Patients were stratified based on their BAC into four categories (undetectable BAC, BAC 1-99mg/dL, BAC 100-199mg/dL, and BAC ≥ 200mg/dL). T-tests and X2 tests were used to detect differences between BAC categories in terms of patient demographics and clinical outcomes. Multivariate linear and logistic regressions were used to investigate the association between patient variables and selected outcomes while controlling for confounders. One third of 738 patients analyzed were BAC-positive, mean (SD) BAC was 211.4 (118.9) mg/dL, 80% of BAC-positive patients had levels ≥ 100mg/dL. After risk adjustments, the following patient characteristics were predictive of having highly elevated BAC (≥200mg/dL) upon admission to the Trauma Center; Hispanic patients (adjusted odds ratio (OR)=1.91, 95% confidence interval (CI): 1.14-3.21), unemployment (OR=1.74, 95% CI: 1.09-2.78), Medicaid beneficiaries (OR=3.59, 95% CI: 1.96-6.59), and uninsured patients (OR=2.86, 95% CI: 1.60-5.13). Patients with BAC of 100-199mg/dL were likely to be more severely injured (P=0.016) compared to undetectable-BAC patients. There was no association between being intoxicated, and being ICU-admitted or having differences in length of ICU or hospital stay. Demographic and socioeconomic factors underlie disparities in the prevalence of alcohol-related trauma among underserved patients. These findings may guide targeted interventions toward specific populations to help reduce the burden of alcohol-related injury. Published by Elsevier Ltd.

Alcohol-related serious road traffic injuries between 2000 and 2010: A new perspective to deal with administrative data in Australia.

PubMed

Ferris, Jason; Killian, Jessica; Lloyd, Belinda

2017-05-01

According to the most recent statistics from the World Health Organization, 1.2 million people die or are injured on the world's roads every year. Drink-driving continues to be a major risk factor for road traffic crashes, with 22% of serious road injuries (SRIs) in Victoria involving a blood alcohol concentration (BAC) equal to or above the legal driving limit of 0.05g/mL. Use of police and hospital data to determine alcohol involvement in SRIs is not reliable, with researchers using proxy measures such as high alcohol hours (HAH). This paper examines patterns of alcohol-related SRIs based on reported BAC versus the surrogate HAH measure. Trends over a 10year period (2000-2010) were examined, comparing four different SRI rates (low alcohol hours (LAH), LAH with positive BAC, HAH, HAH with positive BAC). Discontinuities in the data series were also examined. SRI data were drawn from the Road Networks Database of VicRoads containing information on all reported road crashes in Victoria. For the 10year period there were 52,286 reported SRIs relating to the driver. Of the incidents where a driver's reading was recorded, 44% had a recorded BAC exceeding Victoria's legal limit of 0.05% and a further 23% had a BAC below the legal limit. During the period over 17,000 (or 34%) SRIs occurred during HAH. Where a BAC had been recorded during HAH, almost 60% exceeded the legal limit and a further 20% had some positive recording of BAC. Where SRI drivers had a recorded BAC during LAH, 58% had a positive BAC (31% with a BAC over the legal limit). While it is likely that an SRI occurring during HAH will be associated with a positive BAC (80%), of which 60% will be above the legal limit, almost 60% of SRIs during LAH had a positive BAC, with 31% above the legal limit. There was no significant change in overall alcohol-related SRI rates between 2000 and 2010, suggesting that policies and procedures implemented to decrease drink-driving have not reduced alcohol-related SRI rates. In the absence of a reliable direct measure (i.e., BAC readings) this paper demonstrated the utility of the surrogate HAH measure for determining changes in alcohol-related serious road injuries. Further, the unmet need for routine BAC testing in SRIs occurring during LAH requires further exploration given the significant proportion of SRIs involving positive BAC during these times. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

PubMed

Zheng, Lu; Gao, Naiyun; Deng, Yang

2012-01-01

It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples.

An efficient approach to BAC based assembly of complex genomes.

PubMed

Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; Batley, Jacqueline; Šimková, Hana; Doležel, Jaroslav; Edwards, David

2016-01-01

There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.

Light-activated phenalen-1-one bactericides: efficacy, toxicity and mechanism compared with benzalkonium chloride.

PubMed

Muehler, Denise; Sommer, Kerstin; Wennige, Sara; Hiller, Karl-Anton; Cieplik, Fabian; Maisch, Tim; Späth, Andreas

2017-11-01

Five photoactive compounds with variable elongated alkyl-substituents in a phenalen-1-one structure were examined in view of structural similarity to the antimicrobial agent benzalkonium chloride (BAC). All phenalen-1-ones and BAC were evaluated for their antimicrobial properties against Staphylococcus aureus, methicillin-resistant S. aureus, Escherichia coli, Pseudomonas aeruginosa and for their eukaryotic toxicity against normal human epidermal keratinocyte (NHEK) cells to narrow down the BAC-like effect and the photodynamic effect depending on the chemical structure. All compounds were investigated for effective concentration ranges, where a bacterial reduction of 5 log 10 is achieved, while an NHEK survival of 80% is ensured. Effective concentration ranges were found for four out of five photoactive compounds, but not for BAC and the compound with BAC-like alkyl chain length. Chain length size and polar area of the respective head-groups of phenalen-1-one compounds or BAC showed an influence on the incorporation inside lipid membranes and thus, head-groups may have an impact on the toxicity of antimicrobials.

A physical map of the bovine genome

PubMed Central

Snelling, Warren M; Chiu, Readman; Schein, Jacqueline E; Hobbs, Matthew; Abbey, Colette A; Adelson, David L; Aerts, Jan; Bennett, Gary L; Bosdet, Ian E; Boussaha, Mekki; Brauning, Rudiger; Caetano, Alexandre R; Costa, Marcos M; Crawford, Allan M; Dalrymple, Brian P; Eggen, André; Everts-van der Wind, Annelie; Floriot, Sandrine; Gautier, Mathieu; Gill, Clare A; Green, Ronnie D; Holt, Robert; Jann, Oliver; Jones, Steven JM; Kappes, Steven M; Keele, John W; de Jong, Pieter J; Larkin, Denis M; Lewin, Harris A; McEwan, John C; McKay, Stephanie; Marra, Marco A; Mathewson, Carrie A; Matukumalli, Lakshmi K; Moore, Stephen S; Murdoch, Brenda; Nicholas, Frank W; Osoegawa, Kazutoyo; Roy, Alice; Salih, Hanni; Schibler, Laurent; Schnabel, Robert D; Silveri, Licia; Skow, Loren C; Smith, Timothy PL; Sonstegard, Tad S; Taylor, Jeremy F; Tellam, Ross; Van Tassell, Curtis P; Williams, John L; Womack, James E; Wye, Natasja H; Yang, George; Zhao, Shaying

2007-01-01

Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans. PMID:17697342

Late sampling for automated culture to extend the platelet shelf life to 5 days in Germany.

PubMed

Vollmer, Tanja; Dabisch-Ruthe, Mareike; Weinstock, Melanie; Knabbe, Cornelius; Dreier, Jens

2018-04-15

Bacterial contamination of platelet concentrates (PCs) is still a major challenge in transfusion medicine. Different methodologic concepts and screening strategies have been developed and investigated concerning their usability. We evaluated the feasibility of BacT/ALERT automated culture (BacT/A, bioMérieux) with late sampling after 3 days at the earliest. Twenty-four bacterial strains isolated from PCs and six relevant strains from reference stocks were spiked into apheresis-derived PCs (10-60 colony-forming units [CFU]/bag). Sampling was performed after 3 days, and bacterial detection was investigated using the two detection methods (BacT/A and BactiFlow [BF], bioMérieux). The maximum time-to-result of BacT/A was set to less than 12 hours. All medium- or high-pathogenic strains are capable of proliferating to high titers, and 100% of contaminated samples were detected by BF and BacT/A (6 to ≤12 h incubation); lower detection rates of BacT/A were obtained within 6 hours of incubation (≤6 h: 76.2-93.4%). The majority of low-pathogenic isolates are also capable of growing in PCs (89.7%), showing a detection rate of 74.3% for BF versus 54.3% for BacT/A (6 to ≤12 h incubation). BacT/A failed to detect bacteria within 6 hours of incubation. Certainly, a small number of strains did not grow under PC storage conditions and were detectable by BacT/A only with increased detection times. Late sampling after 3 days at the earliest, combined with reduced BacT/A incubation following the negative-to-date concept, offer an alternative opportunity to extend the shelf life of PCs from 4 to 5 days in Germany. The sensitivity of BacT/A with late sampling is nearly comparable to BF; the time-to-result is considerably longer. © 2018 AABB.

A nanobiohybrid complex of recombinant baculovirus and Tat/DNA nanoparticles for delivery of Ang-1 transgene in myocardial infarction therapy.

PubMed

Paul, Arghya; Binsalamah, Zyad M; Khan, Afshan A; Abbasia, Sana; Elias, Cynthia B; Shum-Tim, Dominique; Prakash, Satya

2011-11-01

The study aims to design a new gene delivery method utilizing the complementary strengths of baculovirus, such as relatively high transduction efficiency and easy scale-up, and non-viral nanodelivery systems, such as low immunogenicity. This formulation was developed by generating a self assembled binary complex of negatively charged baculovirus (Bac) and positively charged endosomolytic histidine rich Tat peptide/DNA nanoparticles (NP). The synergistic effect of this hybrid (Bac-NP) system to induce myocardial angiogenesis in acute myocardial infarction (AMI) model has been explored in this study, using Angiopoietin-1 (Ang-1) as the transgene carried by both vector components. Under optimal transduction conditions, Bac-NP(Ang1) showed 1.75 times higher and sustained Ang-1 expression in cardiomyocytes than Bac(Ang1), with significantly high angiogenic potential as confirmed by functional assays. For in vivo analysis, we intramyocardially delivered Bac-NP(Ang1) to AMI rat model. 3 weeks post AMI, data showed increase in capillary density (p < 0.01) and reduction in infarct sizes (p < 0.05) in Bac-NP(Ang1) compared to Bac(Ang1), NP(Ang1) and control groups due to enhanced myocardial Ang-1 expression at peri-infarct regions (1.65 times higher than Bac(Ang1)). Furthermore, the Bac-NP(Ang1) group showed significantly higher cardiac performance in echocardiography than Bac(Ang1) (44.2 ± 4.77% vs 37.46 ± 5.2%, p < 0.01), NP(Ang1) and the control group (32.26 ± 2.49% and 31.58 ± 2.26%). Collectively, this data demonstrates hybrid Bac-NP as a new and improved gene delivery system for therapeutic applications. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Impact of acute alcohol consumption on lethality of suicide methods.

PubMed

Park, C Hyung Keun; Yoo, Seong Ho; Lee, Jaewon; Cho, Sung Joon; Shin, Min-Sup; Kim, Eun Young; Kim, Se Hyun; Ham, Keunsoo; Ahn, Yong Min

2017-05-01

The influence of acute alcohol consumption on the factors related to suicide remains understudied. Thus, the present study investigated the relationship between blood alcohol content (BAC) and the lethality of suicide methods. Autopsy data on 315 South Korean suicide completers with a positive BAC were collected from a nationwide pool between May 2015 and November 2015, and the methods were dichotomised as suicide methods of low lethality (SMLL; drug/chemical overdose and sharp objects, n=67) and suicide methods of high lethality (SMHL; everything else, n=243). BAC at the time of autopsy and various suicide-related factors of these two groups were compared with logistic regression analyses. Compared to suicide completers with a BAC in the lowest range of 0.011-0.049%, suicide completers with a BAC in the range of 0.150-0.199% were more likely to use SMHL (odds ratio [OR]: 3.644, 95% confidence interval [CI]: 1.221-10.874). Additionally, the adoption of SMHL was significantly associated with the absence of a psychiatric illness (OR: 0.433, 95% CI: 0.222-0.843) and a younger age; the OR for high BAC among subjects in their 40s was 0.266 (95% CI: 0.083-0.856); in their 50s, 0.183 (95% CI: 0.055-0.615); and in their 60s, 0.057 (95% CI: 0.015-0.216). The relationship between BAC and suicide method lethality was represented by a bell-shaped pattern in which suicide methods of high lethality were more likely to be used by suicide completers with mid-range BAC levels. The increased impulsivity and impairments in particular executive functions, including planning and organization, associated with acute alcohol use may influence the selection of a particular suicide method based on its lethality. Copyright © 2017 Elsevier Inc. All rights reserved.

Performance of two resin-containing blood culture media in detection of bloodstream infections and in direct matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) broth assays for isolate identification: clinical comparison of the BacT/Alert Plus and Bactec Plus systems.

PubMed

Fiori, Barbara; D'Inzeo, Tiziana; Di Florio, Viviana; De Maio, Flavio; De Angelis, Giulia; Giaquinto, Alessia; Campana, Lara; Tanzarella, Eloisa; Tumbarello, Mario; Antonelli, Massimo; Sanguinetti, Maurizio; Spanu, Teresa

2014-10-01

We compared the clinical performances of the BacT/Alert Plus (bioMérieux) and Bactec Plus (Becton Dickinson) aerobic and anaerobic blood culture (BC) media with adsorbent polymeric beads. Patients ≥ 16 years old with suspected bloodstream infections (BSIs) were enrolled in intensive care units and infectious disease wards. A single 40-ml blood sample was collected from each and used to inoculate (10 ml/bottle) one set of BacT/Alert Plus cultures and one set of Bactec Plus cultures, each set consisting of one aerobic and one anaerobic bottle. Cultures were incubated ≤ 5 days in the BacT/Alert 3D and Bactec FX instruments, respectively. A total of 128 unique BSI episodes were identified based on the recovery of clinically significant growth in 212 aerobic cultures (106 BacT/Alert and 106 Bactec) and 151 anaerobic cultures (82 BacT/Alert and 69 Bactec). The BacT/Alert aerobic medium had higher recovery rates for Gram-positive cocci (P = 0.024), whereas the Bactec aerobic medium was superior for recovery of Gram-negative bacilli (P = 0.006). BacT/Alert anaerobic medium recovery rates exceeded those of the Bactec anaerobic medium for total organisms (P = 0.003), Gram-positive cocci (P = 0.013), and Escherichia coli (P = 0.030). In terms of capacity for diagnosing the 128 septic episodes, the BacT/Alert and Bactec sets were comparable, although the former sets diagnosed more BSIs caused by Gram-positive cocci (P = 0.008). They also allowed earlier identification of coagulase-negative staphylococcal growth (mean, 2.8 h; P = 0.003) and growth in samples from patients not on antimicrobial therapy that yielded positive results (mean, 1.3 h; P < 0.001). Similarly high percentages of microorganisms in BacT/Alert and Bactec cultures (93.8% and 93.3%, respectively) were identified by direct matrix-assisted laser desorption ionization-time of flight mass spectrometry assay of BC broths. The BacT/Alert Plus media line appears to be a reliable, timesaving tool for routine detection of BSIs in the population we studied, although further studies are needed to evaluate their performance in other settings. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey.

PubMed

Luo, Meizhong; Kim, Hyeran; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A; Ohta, Yuko

2006-05-03

Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

Relationship of Impaired Driving Enforcement Intensity to Drinking and Driving on the Roads

PubMed Central

Fell, James C.; Waehrer, Geetha; Voas, Robert B.; Auld-Owens, Amy; Carr, Katherine; Pell, Karen

2014-01-01

Background It is principally the area of enforcement that offers the greatest opportunity for reducing alcohol-impaired driving in the near future. How much of a reduction in drinking and driving would be achieved by how much improvement in enforcement intensity? Methods We developed logistic regression models to explore how enforcement intensity (six different measures) related to the prevalence of weekend, nighttime drivers in the 2007 National Roadside Survey (NRS) who had been drinking (blood alcohol concentration [BAC]>.00 g/dL), who had BACs>.05 g/dL, and who were driving with an illegal BAC>.08 g/dL. Results Drivers on the roads in our sample of 30 communities who were exposed to fewer than 228 traffic stops per 10,000 population aged 18 and older had 2.4 times the odds of being BAC positive, 3.6 times the odds of driving with a BAC>0.05, and 3.8 times the odds of driving with a BAC>0.08 compared to those drivers on the roads in communities with more than 1,275 traffic stops per 10,000 population. Drivers on the roads in communities with fewer than 3.7 driving-under-the-influence (DUI) arrests per 10,000 population had 2.7 times the odds of BAC-positive drivers on the roads compared to communities with the highest intensity of DUI arrest activity (>38 DUI arrests per 10,000 population). Conclusion The number of traffic stops and DUI arrests per capita were significantly associated with the odds of drinking and driving on the roads in these communities. This might reflect traffic enforcement visibility. The findings in this study may help law enforcement agencies around the country adjust their traffic enforcement intensity to reduce impaired driving in their community. PMID:25515820

Burden of alcohol-related injuries on radiology services at a level I trauma center.

PubMed

Roudsari, Bahman; Psoter, Kevin J; Mack, Christopher; Vavilala, Monica S; Jarvik, Jeffrey G

2012-10-01

The purpose of our study was to evaluate the burden of alcohol-related injuries on a radiology department at a level 1 trauma center. We linked the trauma registry (2005-2009) of Harborview Medical Center to billing department data and extracted patient demographic and injury-related characteristics and the radiology services provided. Multivariate negative binomial analysis was used to evaluate the association between blood alcohol concentration (BAC) and CT and MRI utilization rates. A total of 125,776 CT and 4681 MRI examinations were performed on 27,274 patients during the study period. Higher BAC was generally associated with higher utilization rates for all types of CT even after adjusting for potential confounding variables. Compared with patients with a BAC of 0, the greatest increases in utilization were observed in individuals with a BAC of 240 mg/dL or more for head CT (incidence rate ratio [IRR], 1.43; 95% CI, 1.32-1.54), cervical spine (IRR, 1.45; 95% CI, 1.32-1.58), and maxillofacial (IRR, 1.66; 95% CI, 1.42-1.95), with no increase observed for MRI. This association was more prominent in less severely injured patients with utilization rates for head CT (IRR, 1.83; 95% CI, 1.56-2.13), abdomen (IRR, 1.46; 95% CI, 1.32-1.63), and thorax (IRR, 1.57; 95% CI, 1.30-1.89) in individuals with a BAC of 240 mg/dL or more compared with those with a BAC of 0. Higher BAC was associated with increased CT utilization for most body region-specific CT scans and was more strongly associated in patients with less severe injuries. Any guideline that could potentially decrease unnecessary imaging for patients with alcohol-involved injuries would represent a cost-saving strategy.

A High-throughput AFLP-based Method for Constructing Integrated Genetic and Physical Maps: Progress Toward a Sorghum Genome Map

PubMed Central

Klein, Patricia E.; Klein, Robert R.; Cartinhour, Samuel W.; Ulanch, Paul E.; Dong, Jianmin; Obert, Jacque A.; Morishige, Daryl T.; Schlueter, Shannon D.; Childs, Kevin L.; Ale, Melissa; Mullet, John E.

2000-01-01

Sorghum is an important target for plant genomic mapping because of its adaptation to harsh environments, diverse germplasm collection, and value for comparing the genomes of grass species such as corn and rice. The construction of an integrated genetic and physical map of the sorghum genome (750 Mbp) is a primary goal of our sorghum genome project. To help accomplish this task, we have developed a new high-throughput PCR-based method for building BAC contigs and locating BAC clones on the sorghum genetic map. This task involved pooling 24,576 sorghum BAC clones (∼4× genome equivalents) in six different matrices to create 184 pools of BAC DNA. DNA fragments from each pool were amplified using amplified fragment length polymorphism (AFLP) technology, resolved on a LI-COR dual-dye DNA sequencing system, and analyzed using Bionumerics software. On average, each set of AFLP primers amplified 28 single-copy DNA markers that were useful for identifying overlapping BAC clones. Data from 32 different AFLP primer combinations identified ∼2400 BACs and ordered ∼700 BAC contigs. Analysis of a sorghum RIL mapping population using the same primer pairs located ∼200 of the BAC contigs on the sorghum genetic map. Restriction endonuclease fingerprinting of the entire collection of sorghum BAC clones was applied to test and extend the contigs constructed using this PCR-based methodology. Analysis of the fingerprint data allowed for the identification of 3366 contigs each containing an average of 5 BACs. BACs in ∼65% of the contigs aligned by AFLP analysis had sufficient overlap to be confirmed by DNA fingerprint analysis. In addition, 30% of the overlapping BACs aligned by AFLP analysis provided information for merging contigs and singletons that could not be joined using fingerprint data alone. Thus, the combination of fingerprinting and AFLP-based contig assembly and mapping provides a reliable, high-throughput method for building an integrated genetic and physical map of the sorghum genome. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF218263.] PMID:10854411

Acoustic and Thermal Testing of an Integrated Multilayer Insulation and Broad Area Cooling Shield System

NASA Technical Reports Server (NTRS)

Wood, Jessica J.; Foster, Lee W.

2013-01-01

A Multilayer Insulation (MLI) and Broad Area Cooling (BAC) shield thermal control system shows promise for long-duration storage of cryogenic propellant. The NASA Cryogenic Propellant Storage and Transfer (CPST) project is investigating the thermal and structural performance of this tank-applied integrated system. The MLI/BAC Shield Acoustic and Thermal Test was performed to evaluate the MLI/BAC shield's structural performance by subjecting it to worst-case launch acoustic loads. Identical thermal tests using Liquid Nitrogen (LN2) were performed before and after the acoustic test. The data from these tests was compared to determine if any degradation occurred in the thermal performance of the system as a result of exposure to the acoustic loads. The thermal test series consisted of two primary components: a passive boil-off test to evaluate the MLI performance and an active cooling test to evaluate the integrated MLI/BAC shield system with chilled vapor circulating through the BAC shield tubes. The acoustic test used loads closely matching the worst-case envelope of all launch vehicles currently under consideration for CPST. Acoustic test results yielded reasonable responses for the given load. The thermal test matrix was completed prior to the acoustic test and successfully repeated after the acoustic test. Data was compared and yielded near identical results, indicating that the MLI/BAC shield configuration tested in this series is an option for structurally implementing this thermal control system concept.

Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping.

PubMed

Gaiero, Paola; van de Belt, José; Vilaró, Francisco; Schranz, M Eric; Speranza, Pablo; de Jong, Hans

2017-03-01

A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S. commersonii and S. chachoense pachytene chromosomes, confirming their correspondence with linkage groups in RH potato. Our study shows that the order of BAC signals is conserved. Distances between BAC signals were quantified and compared; some differences found suggest either small-scale rearrangements or reduction/amplification of repeats. We conclude that S. commersonii and S. chacoense are collinear with cultivated Solanum tuberosum on the whole chromosome scale, making these amenable species for efficient introgressive hybridization breeding.

Insect transformation with piggyBac: getting the number of injections just right

PubMed Central

Morrison, N. I.; Shimeld, S. M.

2016-01-01

Abstract The insertion of exogenous genetic cargo into insects using transposable elements is a powerful research tool with potential applications in meeting food security and public health challenges facing humanity. piggyBac is the transposable element most commonly utilized for insect germline transformation. The described efficiency of this process is variable in the published literature, and a comprehensive review of transformation efficiency in insects is lacking. This study compared and contrasted all available published data with a comprehensive data set provided by a biotechnology group specializing in insect transformation. Based on analysis of these data, with particular focus on the more complete observational data from the biotechnology group, we designed a decision tool to aid researchers' decision‐making when using piggyBac to transform insects by microinjection. A combination of statistical techniques was used to define appropriate summary statistics of piggyBac transformation efficiency by species and insect order. Publication bias was assessed by comparing the data sets. The bias was assessed using strategies co‐opted from the medical literature. The work culminated in building the Goldilocks decision tool, a Markov‐Chain Monte‐Carlo simulation operated via a graphical interface and providing guidance on best practice for those seeking to transform insects using piggyBac. PMID:27027400

Performance of a New Rapid Immunoassay Test Kit for Point-of-Care Diagnosis of Significant Bacteriuria

PubMed Central

Cox, Marsha E.; DiNello, Robert K.; Geisberg, Mark; Abbott, April; Roberts, Pacita L.; Hooton, Thomas M.

2015-01-01

Urinary tract infections (UTIs) are frequently encountered in clinical practice and most commonly caused by Escherichia coli and other Gram-negative uropathogens. We tested RapidBac, a rapid immunoassay for bacteriuria developed by Silver Lake Research Corporation (SLRC), compared with standard bacterial culture using 966 clean-catch urine specimens submitted to a clinical microbiology laboratory in an urban academic medical center. RapidBac was performed in accordance with instructions, providing a positive or negative result in 20 min. RapidBac identified as positive 245/285 (sensitivity 86%) samples with significant bacteriuria, defined as the presence of a Gram-negative uropathogen or Staphylococcus saprophyticus at ≥103 CFU/ml. The sensitivities for Gram-negative bacteriuria at ≥104 CFU/ml and ≥105 CFU/ml were 96% and 99%, respectively. The specificity of the test, detecting the absence of significant bacteriuria, was 94%. The sensitivity and specificity of RapidBac were similar on samples from inpatient and outpatient settings, from male and female patients, and across age groups from 18 to 89 years old, although specificity was higher in men (100%) compared with that in women (92%). The RapidBac test for bacteriuria may be effective as an aid in the point-of-care diagnosis of UTIs especially in emergency and primary care settings. PMID:26063858

Characterization of bacterial community and iron corrosion in drinking water distribution systems with O3-biological activated carbon treatment.

PubMed

Xing, Xueci; Wang, Haibo; Hu, Chun; Liu, Lizhong

2018-07-01

Bacterial community structure and iron corrosion were investigated for simulated drinking water distribution systems (DWDSs) composed of annular reactors incorporating three different treatments: ozone, biologically activated carbon and chlorination (O 3 -BAC-Cl 2 ); ozone and chlorination (O 3 -Cl 2 ); or chlorination alone (Cl 2 ). The lowest corrosion rate and iron release, along with more Fe 3 O 4 formation, occurred in DWDSs with O 3 -BAC-Cl 2 compared to those without a BAC filter. It was verified that O 3 -BAC influenced the bacterial community greatly to promote the relative advantage of nitrate-reducing bacteria (NRB) in DWDSs. Moreover, the advantaged NRB induced active Fe(III) reduction coupled to Fe(II) oxidation, enhancing Fe 3 O 4 formation and inhibiting corrosion. In addition, O 3 -BAC pretreatment could reduce high-molecular-weight fractions of dissolved organic carbon effectively to promote iron particle aggregation and inhibit further iron release. Our findings indicated that the O 3 -BAC treatment, besides removing organic pollutants in water, was also a good approach for controlling cast iron corrosion and iron release in DWDSs. Copyright © 2017. Published by Elsevier B.V.

Co-drug strategy for promoting skin targeting and minimizing the transdermal diffusion of hydroquinone and tranexamic acid.

PubMed

Hsieh, Pei-Wen; Chen, Wei-Yu; Aljuffali, Ibrahim A; Chen, Chun-Che; Fang, Jia-You

2013-01-01

Hydroquinone and tranexamic acids (TXA) are skin-lightening agents with a hydrophilic nature and low skin absorption. A high dose is needed for clinical use, resulting in a high incidence of skin irritation. Co-drugs formed by conjugating hydroquinone and TXA were synthesized and their in vitro and in vivo skin absorption characteristics were evaluated. The two synthesized co-drugs were 4-hydroxyphenyl 4-(aminomethyl)cyclohexanecarboxylate (HAC) and 1,4- phenylene bis(aminomethyl)cyclohexanecarboxylate (BAC). The co-drugs were chemically stable in aqueous solution, but rapidly degraded to the respective parent drug in esterases and skin homogenates. Compared to hydroquinone application, 7.2- and 2.4-fold increments in the hydroquinone skin deposition were obtained with the in vitro application of HAC and BAC. HAC and BAC led to 3- and 2-fold enhancements of equivalent TXA deposition compared to TXA administration. The in vivo experiment showed a further enhancement of co-drugs compared to the in vitro setup. The transdermal penetration of co-drugs, especially BAC, was much lower than that of hydroquinone and TXA. This indicated high-level skin targeting by the co-drugs. HAC and BAC revealed strong affinities for the viable epidermis/dermis. Hair follicles are important reservoirs for co-drug delivery. Daily administration of co-drugs to the skin did not generate irritation for up to 7 days. Both co-drugs are superior candidates for treating skin hyperpigmentation.

The relationship between serious injury and blood alcohol concentration (BAC) in fatal motor vehicle accidents: BAC = 0.01% is associated with significantly more dangerous accidents than BAC = 0.00%.

PubMed

Phillips, David P; Brewer, Kimberly M

2011-09-01

To analyze the severity of automotive injuries associated with blood alcohol concentration (BAC) in increments of 0.01%. Epidemiological study using the Fatality Analysis Reporting System. All people in US fatal automotive accidents, 1994-2008 (n = 1 495 667). The ratio of serious: non-serious injuries for drivers, by BAC. Accident severity increases significantly even when the driver is merely 'buzzed', a finding that persists after standardization for various confounding factors. Three mechanisms mediate between buzzed driving and high accident severity: compared to sober drivers, buzzed drivers are significantly more likely to speed, to be improperly seatbelted and to drive the striking vehicle. In addition, there is a strong 'dose-response' relationship for all three factors in relation to accident severity (e.g. the greater the BAC, the greater the average speed of the driver and the greater the severity of the accident). The severity of life-threatening motor vehicle accidents increases significantly at blood alcohol concentrations (BACs) far lower than the current US limit of 0.08%. Lowering the legal limit could save lives, prevent serious injuries and reduce financial and social costs associated with motor vehicle accidents. © 2011 Society for the Study of Addiction. No claim to original US government works.

The antimicrobial effect of benzalkonium chloride on some pathogenic microbes observed on fibers of acrylic carpet.

PubMed

Khajavi, Ramin; Sattari, Morteza; Ashjaran, Ali

2007-02-15

In the presented research, the main aim is to investigate the antibacterial effectiveness of BAC solutions on acrylic fibers used in machinery carpet. An acrylic pile carpet laid in a public place for 30 days and the existence of some microbes were investigated on it. The antimicrobial effect of different BAC solutions for identified microbes was studied in vitro. The acrylic fibers were treated with the same different solutions of BAC as before and the antibacterial effectiveness was assessed by the zone of inhibition method in different times. Two pieces of carpet untreated and treated with BAC solution sewed together and laid for one week in the public place and the amounts of bacterial growth determined by colony count method and the results compared. Finally some mechanical properties of treated acrylic fibers measured after 30 days and compared with untreated one. The results showed the presence of some pathogenic microbes on the laid carpet such as Escherichia coli and Staphylococcus aureus. The inhalation time for treated acrylic fibers improved. The amount of colony growth on treated carpet reduced considerably and besides the mechanical tests results showed no significant deterioration effect of studied properties in comparing with untreated yarn.

Validation of the French version of the BACS (the brief assessment of cognition in schizophrenia) among 50 French schizophrenic patients.

PubMed

Bralet, Marie-Cécile; Falissard, Bruno; Neveu, Xavier; Lucas-Ross, Margaret; Eskenazi, Anne-Marie; Keefe, Richard S E

2007-09-01

Schizophrenic patients demonstrate impairments in several key dimensions of cognition. These impairments are correlated with important aspects of functional outcome. While assessment of these cognition disorders is increasingly becoming a part of clinical and research practice in schizophrenia, there is no standard and easily administered test battery. The BACS (Brief Assessment of Cognition in Schizophrenia) has been validated in English language [Keefe RSE, Golberg TE, Harvey PD, Gold JM, Poe MP, Coughenour L. The Brief Assessment of Cognition in Schizophrenia: reliability, sensibility, and comparison with a standard neurocognitive battery. Schizophr. Res 2004;68:283-97], and was found to be as sensitive to cognitive dysfunction as a standard battery of tests, with the advantage of requiring less than 35 min to complete. We developed a French adaptation of the BACS and this study tested its ease of administration and concurrent validity. Correlation analyses between the BACS (version A) and a standard battery were performed. A sample of 50 stable schizophrenic patients received the French Version A of the BACS in a first session, and in a second session a standard battery. All the patients completed each of the subtests of the French BACS . The mean duration of completion for the BACS French version was 36 min (S.D.=5.56). A correlation analysis between the BACS (version A) global score and the standard battery global score showed a significant result (r=0.81, p<0.0001). The correlation analysis between the BACS (version A) sub-scores and the standard battery sub-scores showed significant results for verbal memory, working memory, verbal fluency, attention and speed of information processing and executive functions (p<0.001) and for motor speed (p<0.05). The French Version of the BACS is easier to use in French schizophrenic patients compared to a standard battery (administration shorter and completion rate better) and its good psychometric properties suggest that the French Version of the BACS may be a useful tool for assessing cognition in schizophrenic patients with French as their primary language.

Results of a Randomized Controlled Multicenter Phase III Trial of Percutaneous Hepatic Perfusion Compared with Best Available Care for Patients with Melanoma Liver Metastases.

PubMed

Hughes, Marybeth S; Zager, Jonathan; Faries, Mark; Alexander, H Richard; Royal, Richard E; Wood, Bradford; Choi, Junsung; McCluskey, Kevin; Whitman, Eric; Agarwala, Sanjiv; Siskin, Gary; Nutting, Charles; Toomey, Mary Ann; Webb, Carole; Beresnev, Tatiana; Pingpank, James F

2016-04-01

There is no consensus for the treatment of melanoma metastatic to the liver. Percutaneous hepatic perfusion with melphalan (PHP-Mel) is a method of delivering regional chemotherapy selectively to the liver. In this study, we report the results of a multicenter, randomized controlled trial comparing PHP-Mel with best alternative care (BAC) for patients with ocular or cutaneous melanoma metastatic to the liver. A total of 93 patients were randomized to PHP-Mel (n = 44) or BAC (n = 49). On the PHP-Mel arm, melphalan was delivered via the hepatic artery, and the hepatic effluent captured and filtered extracorporeally prior to return to the systemic circulation via a venovenous bypass circuit. PHP-Mel was repeatable every 4-8 weeks. The primary endpoint was hepatic progression-free survival (hPFS), and secondary endpoints included overall PFS (oPFS), overall survival (OS), hepatic objective response (hOR), and safety. hPFS was 7.0 months for PHP-Mel and 1.6 months for BAC (p < 0.0001), while oPFS was 5.4 months for PHP-Mel and 1.6 months for BAC (p < 0.0001). Median OS was not significantly different (PHP-Mel 10.6 months vs. BAC 10.0 months), likely due to crossover to PHP-Mel treatment (57.1 %) from the BAC arm, and the hOR was 36.4 % for PHP-Mel and 2.0 % for BAC (p < 0.001). The majority of adverse events were related to bone marrow suppression. Four deaths were attributed to PHP-Mel, three in the primary PHP-Mel group, and one post-crossover to PHP-Mel from BAC. This randomized, phase III study demonstrated the efficacy of the PHP-Mel procedure. hPFS, oPFS, and hOR were significantly improved with PHP-Mel. PHP with melphalan should provide a new treatment option for unresectable metastatic melanoma in the liver.

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

EPA Science Inventory

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing. Here, we evaluated ten of these methods (BacH, BacHum-UCD, B. thetaiotaomic...

The mucosal toxicity of different benzalkonium chloride analogues evaluated with an alternative test using slugs.

PubMed

Adriaens, E; Dierckens, K; Bauters, T G; Nelis, H J; van Goethem, F; Vanparys, P; Remon, J P

2001-07-01

The objective of this study was to evaluate the mucosal toxicity of different benzalkonium chloride (BAC) analogues using slugs as the alternative test organism. The effect of different BAC analogues on the mucosal tissue of slugs was determined from the protein, lactate dehydrogenase, and alkaline phosphatase released from the foot mucosa after treatment. Additionally, mucus production and reduction in body weight of the slugs were measured. The eye irritation potency of the molecules was evaluated with the Bovine Corneal Opacity and Permeability (BCOP) assay. The antimicrobial activity of the different BAC analogues was also assessed. All BAC analogues induced severe damage to the mucosal epithelium of the slugs, and the irritation increased with decreasing alkyl chain length: BAC-C16 < BAC-C14 < BAC-C12 approximately BAC-mix. A similar ranking was obtained with the BCOP assay for eye irritation. The relative order of activities among the three BAC analogues was the same, i.e., BAC-C14 > or = BAC-C16 > BAC-C12. The BAC-C14 exhibited higher activity than the BAC-mix. The toxicity and activity of BAC analogues depend on the alkyl chain length. The use of BAC-C14 as a conservative agent in pharmaceutical preparations instead of the BAC-mix should be considered.

Extensive Conserved Synteny of Genes between the Karyotypes of Manduca sexta and Bombyx mori Revealed by BAC-FISH Mapping

PubMed Central

Tanaka-Okuyama, Makiko; Shibata, Fukashi; Yoshido, Atsuo; Marec, František; Wu, Chengcang; Zhang, Hongbin; Goldsmith, Marian R.

2009-01-01

Background Genome sequencing projects have been completed for several species representing four highly diverged holometabolous insect orders, Diptera, Hymenoptera, Coleoptera, and Lepidoptera. The striking evolutionary diversity of insects argues a need for efficient methods to apply genome information from such models to genetically uncharacterized species. Constructing conserved synteny maps plays a crucial role in this task. Here, we demonstrate the use of fluorescence in situ hybridization with bacterial artificial chromosome probes as a powerful tool for physical mapping of genes and comparative genome analysis in Lepidoptera, which have numerous and morphologically uniform holokinetic chromosomes. Methodology/Principal Findings We isolated 214 clones containing 159 orthologs of well conserved single-copy genes of a sequenced lepidopteran model, the silkworm, Bombyx mori, from a BAC library of a sphingid with an unexplored genome, the tobacco hornworm, Manduca sexta. We then constructed a BAC-FISH karyotype identifying all 28 chromosomes of M. sexta by mapping 124 loci using the corresponding BAC clones. BAC probes from three M. sexta chromosomes also generated clear signals on the corresponding chromosomes of the convolvulus hawk moth, Agrius convolvuli, which belongs to the same subfamily, Sphinginae, as M. sexta. Conclusions/Significance Comparison of the M. sexta BAC physical map with the linkage map and genome sequence of B. mori pointed to extensive conserved synteny including conserved gene order in most chromosomes. Only a few rearrangements, including three inversions, three translocations, and two fission/fusion events were estimated to have occurred after the divergence of Bombycidae and Sphingidae. These results add to accumulating evidence for the stability of lepidopteran genomes. Generating signals on A. convolvuli chromosomes using heterologous M. sexta probes demonstrated that BAC-FISH with orthologous sequences can be used for karyotyping a wide range of related and genetically uncharacterized species, significantly extending the ability to develop synteny maps for comparative and functional genomics. PMID:19829706

The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS

PubMed Central

Almuhayawi, Mohammed; Altun, Osman; Abdulmajeed, Adam Dilshad; Ullberg, Måns; Özenci, Volkan

2015-01-01

Detection and identification of anaerobic bacteria in blood cultures (BC) is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux), BACTEC-Plus and -Lytic (Becton Dickinson BioSciences) BC bottles in detection and time to detection (TTD) of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94%) than BacT/ALERT FN Plus (80/100, 80%) (p<0.01) in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD) and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001). The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h), BACTEC Plus (27 h) and finally BacT/ALERT FN Plus (38 h) bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76%) BacT/ALERT FN, 51/67 (76%) BacT/ALERT FN Plus, 53/67 (79%) BACTEC Plus and 50/67 (75%) BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS. PMID:26554930

The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS.

PubMed

Almuhayawi, Mohammed; Altun, Osman; Abdulmajeed, Adam Dilshad; Ullberg, Måns; Özenci, Volkan

2015-01-01

Detection and identification of anaerobic bacteria in blood cultures (BC) is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux), BACTEC-Plus and -Lytic (Becton Dickinson BioSciences) BC bottles in detection and time to detection (TTD) of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94%) than BacT/ALERT FN Plus (80/100, 80%) (p<0.01) in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD) and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001). The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h), BACTEC Plus (27 h) and finally BacT/ALERT FN Plus (38 h) bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76%) BacT/ALERT FN, 51/67 (76%) BacT/ALERT FN Plus, 53/67 (79%) BACTEC Plus and 50/67 (75%) BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

PubMed Central

2009-01-01

Background Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. Results We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR) and a cytochrome P450 (CYP720B4) from a non-arrayed genomic BAC library of white spruce (Picea glauca). Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR) and 94 kbp (CYP720B4) long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs), high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. Conclusion We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene families can be isolated in a gene-specific fashion. The results of the present work provide important new information about the structure and content of conifer genomic DNA that will guide future efforts to sequence and assemble conifer genomes. PMID:19656416

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome.

PubMed

Hamberger, Björn; Hall, Dawn; Yuen, Mack; Oddy, Claire; Hamberger, Britta; Keeling, Christopher I; Ritland, Carol; Ritland, Kermit; Bohlmann, Jörg

2009-08-06

Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR) and a cytochrome P450 (CYP720B4) from a non-arrayed genomic BAC library of white spruce (Picea glauca). Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR) and 94 kbp (CYP720B4) long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs), high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene families can be isolated in a gene-specific fashion. The results of the present work provide important new information about the structure and content of conifer genomic DNA that will guide future efforts to sequence and assemble conifer genomes.

Effects of enhanced sanctions for high-BAC DWI offenders on case dispositions and rates of recidivism.

PubMed

McCartt, Anne T; Shabanova, Veronika I

2002-01-01

High-BAC sanctioning systems seek to reduce recidivism among a high-risk group of impaired drivers. Minnesota's 1998 high-BAC law imposes more severe administrative and court sanctions on offenders with BAC> or =.20 than on offenders with BAC<.20. After the law, high-BAC first-time and repeat offenders did, in fact, receive more severe case dispositions (e.g., longer license revocation, stronger vehicle sanctions) than lower-BAC offenders. Alcohol test refusals declined. The severity of sanctions for high-BAC offenders declined in 1999 vs. 1998, especially for BACs.20-.22. Recidivism for high-BAC first offenders in 1998 was lower than for offenders with BACs.17-19.

High-resolution human/goat comparative map of the goat polled/intersex syndrome (PIS): the human homologue is contained in a human YAC from HSA3q23.

PubMed

Vaiman, D; Schibler, L; Oustry-Vaiman, A; Pailhoux, E; Goldammer, T; Stevanovic, M; Furet, J P; Schwerin, M; Cotinot, C; Fellous, M; Cribiu, E P

1999-02-15

The genetic and cytogenetic map around the chromosome 1 region shown to be linked with polledness and intersexuality (PIS) in the domestic goat (Capra hircus) was refined. For this purpose, a goat BAC library was systematically screened with primers from human coding sequences, scraped chromosome 1 DNA, bovine microsatellites from the region, and BAC ends. All the BACs (n = 30) were mapped by fluorescence in situ hybridization (FISH) on goat chromosome 1q41-q45. The genetic mapping of 30 new goat polymorphic markers, isolated from these BACs, made it possible to reduce the PIS interval to a region of less than 1 cM on goat chromosome 1q43. The PIS locus is now located between the two genes ATP1B and COP, which both map to 3q23 in humans. Genetic, cytogenetic, and comparative data suggest that the PIS region is now probably circumscribed to an approximately 1-Mb DNA segment for which construction of a BAC contig is in progress. In addition, a human YAC contig encompassing the blepharophimosis-ptosis-epicanthus-inversus region was mapped by FISH to goat chromosome 1q43. This human disease, mapped to HSA 3q23 and affecting the development and maintenance of ovarian function, could be a potential candidate for goat PIS. Copyright 1999 Academic Press.

Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing

PubMed Central

2011-01-01

Background Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. Recent interest is being directed at NLL to improve grain production, disease and pest management and health benefits of the grain. However, studies have been hindered by a lack of extensive genomic resources for the species. Results A NLL BAC library was constructed consisting of 111,360 clones with an average insert size of 99.7 Kbp from cv Tanjil. The library has approximately 12 × genome coverage. Both ends of 9600 randomly selected BAC clones were sequenced to generate 13985 BAC end-sequences (BESs), covering approximately 1% of the NLL genome. These BESs permitted a preliminary characterisation of the NLL genome such as organisation and composition, with the BESs having approximately 39% G:C content, 16.6% repetitive DNA and 5.4% putative gene-encoding regions. From the BESs 9966 simple sequence repeat (SSR) motifs were identified and some of these are shown to be potential markers. Conclusions The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for the species. PMID:22014081

Performance of the BacT Alert 3D System Versus Solid Media for Recovery and Drug Susceptibility Testing of Mycobacterium tuberculosis in a Tertiary Hospital in Korea.

PubMed

Kim, Seoung-Cheol; Jeon, Bo-Young; Kim, Jin-Sook; Choi, In Hwan; Kim, Jiro; Woo, Jeongim; Kim, Soojin; Lee, Hyeong Woo; Sezim, Monoldorova; Cho, Sang-Nae

2016-10-01

Tuberculosis (TB) is a major health problem, and accurate and rapid diagnosis of multidrug-resistant (MDR) and extended drug-resistant (XDR) TB is important for appropriate treatment. In this study, performances of solid and liquid culture methods were compared with respect to MDR- and XDR-TB isolate recovery and drug susceptibility testing. Sputum specimens from 304 patients were stained with Ziehl-Neelsen method. Mycobacterium tuberculosis (Mtb) isolates were tested for recovery on Löwenstein-Jensen (LJ) medium and the BacT Alert 3D system. For drug susceptibility testing of Mtb, isolates were evaluated on M-KIT plates and the BacT Alert 3D system. The recovery rates were 94.9% (206/217) and 98.2% (213/217) for LJ medium and the BacT Alert 3D system, respectively (kappa coefficient, 0.884). The rate of drug resistance was 13.4% for at least one or more drugs, 6.0% for MDR-TB and 2.3% for XDR-TB. M-KIT plate and BacT 3D Alert 3D system were comparable in drug susceptibility testing for isoniazid (97.7%; kappa coefficient, 0.905) and rifampin (98.6%; kappa coefficient, 0.907). Antibiotic resistance was observed using M-KIT plates for 24 of the total 29 Mtb isolates (82.8%). The liquid culture system showed greater reduction in the culture period, as compared with LJ medium; however, drug susceptibility testing using M-KIT plates was advantageous for simultaneous testing against multiple drug targets.

Daily Associations Between Alcohol Consumption and Dating Violence Perpetration Among Men and Women: Effects of Self-Regulation.

PubMed

Stappenbeck, Cynthia A; Gulati, Natasha K; Fromme, Kim

2016-01-01

Alcohol intoxication has been associated with dating violence perpetration, defined here as psychological and/or physical violence occurring between young adult dating partners. However, little is known about how the individual variability in the level of alcohol intoxication would influence dating violence perpetration and how sex and self-regulation might influence this association. College-aged men and women (N = 146) from a large southwestern U.S. university completed background questionnaires, including the Brief Self-Control Scale, to assess self-regulation and then reported their dating violence perpetration and alcohol consumption using a 90-day Timeline Followback assessment. Their average estimated blood alcohol concentration (eBAC) and their daily deviation from this average were calculated for each of the 90 days to examine the between- and within-person effects of alcohol consumption, respectively. Results of a two-level generalized estimating equation suggest that increases in daily eBAC were associated with an increased likelihood of perpetrating dating violence; however, this association was stronger for those who had a low average eBAC compared with those who had a high average eBAC. For those who had a low average eBAC, higher self-regulation was associated with a lower probability of perpetrating dating violence, whereas among those with a high average eBAC, self-regulation was not associated with dating violence perpetration. Sex did not moderate the association between eBAC and dating violence perpetration. Findings highlight the importance of self-regulation in dating violence perpetration-particularly for those with low average eBACs-and the need for varied intervention strategies, depending on one's typical drinking pattern.

Cross-species bacterial artificial chromosome (BAC) library screening via overgo-based hybridization and BAC-contig mapping of a yield enhancement quantitative trait locus (QTL) yld1.1 in the Malaysian wild rice Oryza rufipogon.

PubMed

Song, Beng-Kah; Nadarajah, Kalaivani; Romanov, Michael N; Ratnam, Wickneswari

2005-01-01

The construction of BAC-contig physical maps is an important step towards a partial or ultimate genome sequence analysis. Here, we describe our initial efforts to apply an overgo approach to screen a BAC library of the Malaysian wild rice species, Oryza rufipogon. Overgo design is based on repetitive element masking and sequence uniqueness, and uses short probes (approximately 40 bp), making this method highly efficient and specific. Pairs of 24-bp oligos that contain an 8-bp overlap were developed from the publicly available genomic sequences of the cultivated rice, O. sativa, to generate 20 overgo probes for a 1-Mb region that encompasses a yield enhancement QTL yld1.1 in O. rufipogon. The advantages of a high similarity in melting temperature, hybridization kinetics and specific activities of overgos further enabled a pooling strategy for library screening by filter hybridization. Two pools of ten overgos each were hybridized to high-density filters representing the O. rufipogon genomic BAC library. These screening tests succeeded in providing 69 PCR-verified positive hits from a total of 23,040 BAC clones of the entire O. rufipogon library. A minimal tilling path of clones was generated to contribute to a fully covered BAC-contig map of the targeted 1-Mb region. The developed protocol for overgo design based on O. sativa sequences as a comparative genomic framework, and the pooled overgo hybridization screening technique are suitable means for high-resolution physical mapping and the identification of BAC candidates for sequencing.

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

PubMed Central

2011-01-01

Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed. PMID:21794110

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.

PubMed

Feltus, Frank A; Saski, Christopher A; Mockaitis, Keithanne; Haiminen, Niina; Parida, Laxmi; Smith, Zachary; Ford, James; Staton, Margaret E; Ficklin, Stephen P; Blackmon, Barbara P; Cheng, Chun-Huai; Schnell, Raymond J; Kuhn, David N; Motamayor, Juan-Carlos

2011-07-27

BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

Moderate alcohol intake and motor vehicle crashes: the conflict between health advantage and at-risk use.

PubMed

Heng, Kenneth; Hargarten, Stephen; Layde, Peter; Craven, Andy; Zhu, Shankuan

2006-01-01

To review the evidence on moderate alcohol intake and motor vehicle crash (MVC) risk, and discuss the possible public health tension in balancing risk reduction and increment with respect to moderate alcohol intake. A Medline review was conducted on moderate alcohol intake, MVC, and cardiovascular disease (CVD) risks. Moderate alcohol intake (24 g ethanol, two US standard drinks, or less a day) is associated with 20% reduction in risk of CVD. Public awareness of this may contribute to why rates of driving with blood alcohol content (BAC) <0.08 g/dl in the United States are static. Studies show 3- to 17-fold increased risk of a fatal MVC with BAC < 0.08 g/dl compared to sober drivers. The United States has 0.08 g/dl BAC laws, higher than that reached by a driver drinking two drinks per day or less. The public should be educated that although moderate alcohol drinking may not violate BAC laws, it still carries significant risk of MVC. Current BAC laws in some countries needs re-evaluation.

Alignment of the Genomes of Brachypodium distachyon and Temperate Cereals and Grasses Using Bacterial Artificial Chromosome Landing With Fluorescence in Situ Hybridization

PubMed Central

Hasterok, Robert; Marasek, Agnieszka; Donnison, Iain S.; Armstead, Ian; Thomas, Ann; King, Ian P.; Wolny, Elzbieta; Idziak, Dominika; Draper, John; Jenkins, Glyn

2006-01-01

As part of an initiative to develop Brachypodium distachyon as a genomic “bridge” species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice. PMID:16489232

Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization.

PubMed

Hasterok, Robert; Marasek, Agnieszka; Donnison, Iain S; Armstead, Ian; Thomas, Ann; King, Ian P; Wolny, Elzbieta; Idziak, Dominika; Draper, John; Jenkins, Glyn

2006-05-01

As part of an initiative to develop Brachypodium distachyon as a genomic "bridge" species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice.

Ethylglucuronide in hair is a top predictor of impaired driving recidivism, alcohol dependence, and a key marker of the highest BAC interlock tests.

PubMed

Marques, Paul R; Tippetts, A Scott; Yegles, Michel

2014-01-01

This study focuses on the predictive and comparative significance of ethyl glucuronide measured in head hair (hEtG) for estimating risks associated with alcohol-impaired driving offenders. Earlier work compared different alcohol biomarkers for estimating rates of failed blood alcohol concentration (BAC) tests logged during 8 months of interlock participation. These analyses evaluate the comparative performance of several alcohol markers including hEtG and other markers, past driver records, and psychometric assessment predictors for the detection of 4 criteria: new driving under the influence (DUI) recidivism, alcohol dependence, and interlock record variables including fail rates and maximal interlock BACs logged. Drivers charged with alcohol impairment (DUI) in Alberta, Canada (n = 534; 64% first offenders, 36% multiple offenders) installed ignition interlock devices and consented to participate in research to evaluate blood-, hair-, and urine-derived alcohol biomarkers; sit for interviews; take psychometric assessments; and permit analyses of driving records and interlock log files. Subject variables included demographics, alcohol dependence at program entry, preprogram prior DUI convictions, postenrollment new DUI convictions, self-reported drinking assessments, morning and overall rates of failed interlock BAC tests, and maximal interlock BAC readings. Recidivism, dependence, high BAC, and combined fail rates were set as criteria; other variables were set as predictors. Area under the receiver operating characteristics (ROC) curve (A') estimates of sensitivity and specificity were calculated. Additional analyses were conducted on baseline hEtG levels. Driver performance and drinking indicators were evaluated against the standard hEtG cutoff for excessive drinking at (30 pg/mg) and a higher criterion of 50 pg/mg. HEtG splits were evaluated with the Mann-Whitney rank statistic. HEtG emerged as a top overall predictor for discriminating new recidivism events that occur after interlock installation, for entry alcohol dependence, and for the highest interlock BACs recorded. Together, hEtG and phosphatidylethanol (PEth) were the top predictors of all criterion measures. By contrast, the hair-derived alcohol biomarkers hEtG and hFAEE (fatty acid ethyl esters) were poorer than other alcohol biomarkers as detectors of interlock BAC test fail rates. This study showed that hEtG, an objective alternative to often unreliable self-reported past representation of drinking levels, yields crucial insight into driver alcohol-related risks early in an interlock program and is a top predictor of new recidivist events. Together with PEth, these markers would be excellent anchors in a panel for detecting alcohol consumption.

Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains.

PubMed

Kurushima, Jun; Ike, Yasuyoshi; Tomita, Haruyoshi

2016-09-01

Bacteriocin 41 (Bac41) is the plasmid-encoded bacteriocin produced by the opportunistic pathogen Enterococcus faecalis Its genetic determinant consists of bacL1 (effector), bacL2 (regulator), bacA (effector), and bacI (immunity). The secreted effectors BacL1 and BacA coordinate to induce the lytic cell death of E. faecalis Meanwhile, the immunity factor BacI provides self-resistance to the Bac41 producer, E. faecalis, against the action of BacL1 and BacA. In this study, we demonstrated that more than half of the 327 clinical strains of E. faecalis screened had functional Bac41 genes. Analysis of the genetic structure of the Bac41 genes in the DNA sequences of the E. faecalis strains revealed that the Bac41-like genes consist of a relatively conserved region and a variable region located downstream from bacA Based on similarities in the variable region, the Bac41-like genes could be classified into type I, type IIa, and type IIb. Interestingly, the distinct Bac41 types had specific immunity factors for self-resistance, BacI1 or BacI2, and did not show cross-immunity to the other type of effector. We also demonstrated experimentally that the specificity of the immunity was determined by the combination of the C-terminal region of BacA and the presence of the unique BacI1 or BacI2 factor. These observations suggested that Bac41-like bacteriocin genes are extensively disseminated among E. faecalis strains in the clinical environment and can be grouped into at least three types. It was also indicated that the partial diversity results in specificity of self-resistance which may offer these strains a competitive advantage. Bacteriocins are antibacterial effectors produced by bacteria. In general, a bacteriocin-coding gene is accompanied by a cognate immunity gene that confers self-resistance on the bacteriocin-producing bacterium itself. We demonstrated that one of the bacteriocins, Bac41, is disseminated among E. faecalis clinical strains and the Bac41 subtypes with partial diversity. The Bac41-like bacteriocins were found to be classified into type I, type IIa, and type IIb by variation of the cognate immunity factors. The antibacterial activity of the respective effectors was specifically inhibited by the immunity factor from the same type of Bac41 but not the other types. This specificity of effector-immunity pairs suggests that bacteriocin genes might have evolved to change the immunity specificity to acquire an advantage in interbacterial competition. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Bond additivity corrections for quantum chemistry methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

C. F. Melius; M. D. Allendorf

1999-04-01

In the 1980's, the authors developed a bond-additivity correction procedure for quantum chemical calculations called BAC-MP4, which has proven reliable in calculating the thermochemical properties of molecular species, including radicals as well as stable closed-shell species. New Bond Additivity Correction (BAC) methods have been developed for the G2 method, BAC-G2, as well as for a hybrid DFT/MP2 method, BAC-Hybrid. These BAC methods use a new form of BAC corrections, involving atomic, molecular, and bond-wise additive terms. These terms enable one to treat positive and negative ions as well as neutrals. The BAC-G2 method reduces errors in the G2 method duemore » to nearest-neighbor bonds. The parameters within the BAC-G2 method only depend on atom types. Thus the BAC-G2 method can be used to determine the parameters needed by BAC methods involving lower levels of theory, such as BAC-Hybrid and BAC-MP4. The BAC-Hybrid method should scale well for large molecules. The BAC-Hybrid method uses the differences between the DFT and MP2 as an indicator of the method's accuracy, while the BAC-G2 method uses its internal methods (G1 and G2MP2) to provide an indicator of its accuracy. Indications of the average error as well as worst cases are provided for each of the BAC methods.« less

Reducing false positives of microcalcification detection systems by removal of breast arterial calcifications.

PubMed

Mordang, Jan-Jurre; Gubern-Mérida, Albert; den Heeten, Gerard; Karssemeijer, Nico

2016-04-01

In the past decades, computer-aided detection (CADe) systems have been developed to aid screening radiologists in the detection of malignant microcalcifications. These systems are useful to avoid perceptual oversights and can increase the radiologists' detection rate. However, due to the high number of false positives marked by these CADe systems, they are not yet suitable as an independent reader. Breast arterial calcifications (BACs) are one of the most frequent false positives marked by CADe systems. In this study, a method is proposed for the elimination of BACs as positive findings. Removal of these false positives will increase the performance of the CADe system in finding malignant microcalcifications. A multistage method is proposed for the removal of BAC findings. The first stage consists of a microcalcification candidate selection, segmentation and grouping of the microcalcifications, and classification to remove obvious false positives. In the second stage, a case-based selection is applied where cases are selected which contain BACs. In the final stage, BACs are removed from the selected cases. The BACs removal stage consists of a GentleBoost classifier trained on microcalcification features describing their shape, topology, and texture. Additionally, novel features are introduced to discriminate BACs from other positive findings. The CADe system was evaluated with and without BACs removal. Here, both systems were applied on a validation set containing 1088 cases of which 95 cases contained malignant microcalcifications. After bootstrapping, free-response receiver operating characteristics and receiver operating characteristics analyses were carried out. Performance between the two systems was compared at 0.98 and 0.95 specificity. At a specificity of 0.98, the sensitivity increased from 37% to 52% and the sensitivity increased from 62% up to 76% at a specificity of 0.95. Partial areas under the curve in the specificity range of 0.8-1.0 were significantly different between the system without BACs removal and the system with BACs removal, 0.129 ± 0.009 versus 0.144 ± 0.008 (p<0.05), respectively. Additionally, the sensitivity at one false positive per 50 cases and one false positive per 25 cases increased as well, 37% versus 51% (p<0.05) and 58% versus 67% (p<0.05) sensitivity, respectively. Additionally, the CADe system with BACs removal reduces the number of false positives per case by 29% on average. The same sensitivity at one false positive per 50 cases in the CADe system without BACs removal can be achieved at one false positive per 80 cases in the CADe system with BACs removal. By using dedicated algorithms to detect and remove breast arterial calcifications, the performance of CADe systems can be improved, in particular, at false positive rates representative for operating points used in screening.

Comparative chromosomal localization of the canine-derived BAC clones containing LEP and IGF1 genes in four species of the family Canidae.

PubMed

Szczerbal, I; Rogalska-Niznik, N; Klukowska, J; Schelling, C; Dolf, G; Switonski, M

2003-01-01

In the present report we show the chromosomal localization of two BAC clones, carrying the leptin (LEP) and insuline-like growth factor 1 (IGF1) genes, respectively, in four species belonging to the family Canidae: the dog, red fox, arctic fox and the Chinese raccoon dog. The assignments are in agreement with earlier data obtained from comparative chromosome painting for the dog, red fox and arctic fox. Copyright 2003 S. Karger AG, Basel

Effect of advanced oxidation on N-nitrosodimethylamine (NDMA) formation and microbial ecology during pilot-scale biological activated carbon filtration.

PubMed

Li, Dong; Stanford, Ben; Dickenson, Eric; Khunjar, Wendell O; Homme, Carissa L; Rosenfeldt, Erik J; Sharp, Jonathan O

2017-04-15

Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H 2 O 2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H 2 O 2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated. While microbial populations were highly similar in the upper reaches, deeper samples revealed a divergence within and between BAC filtration systems where EBCT was identified to be a significant environmental predictor for shifts in microbial populations. The abundance of Nitrospira in the top samples of both columns provides an explanation for the oxidation of nitrite and corresponding increases in nitrate concentrations during BAC transit and support interplay between nitrogen cycling with nitrosamine formation. The results of this study demonstrate that pretreatments using ozone versus UV/H 2 O 2 impart modest differences to the overall BAC microbial population structural and functional attributes, and further highlight the need to evaluate NDMA formation prior to full-scale implementation of BAC in potable reuse applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Enhanced broadband near-IR luminescence and gain spectra of bismuth/erbium co-doped fiber by 830 and 980 nm dual pumping

NASA Astrophysics Data System (ADS)

Zhao, Qiancheng; Luo, Yanhua; Wang, Wenyu; Canning, John; Peng, Gang-Ding

2017-04-01

A dual 830 and 980 nm pumping scheme is proposed aiming at broadening and flattening the spectral performance of bismuth/erbium codoped multicomponent fiber (BEDF). The spectral properties of distinct Bi active centers (BACs) associated with germanium (BAC-Ge), aluminium (BAC-Al), phosphorus (BAC-P) and silicon (BAC-Si) are characterized under single pumping of 830 and 980 nm, respectively. Based on the emission slope efficiencies of BAC-Al (˜1100 nm) and BAC-Si (˜1430 nm) under single pumping of 830 and 980 nm, the dual pumping scheme with the optimal pump power ratio of 25 (980 nm VS 830 nm) is determined to achieve flat, ultrabroadband luminescence spectra covering the wavelength range 950-1600 nm. The dual pumping scheme is further demonstrated on the on-off gain performance of BEDF. It is found under the pump power ratio of ˜8 (980 VS 830 nm), The gain spectrum has been flattened and broadened over 300 nm (1300-1600 nm) with an average gain coefficient of ˜1.5 dBm-1. The spectral coverage is approximately 1.5 and 3 times wider compared to single pumping of 830 and 980 nm pumping, respectively. The energy level diagrams of 830 and 980 nm are also constructed separately in view of the optical characteristic, which further clarifies the advantage for dual pumping. The proposed dual 830 and 980 nm pumping scheme with the multicomponent BEDF shows great potential in various broadband optical applications such as uniform ASE source, broadband amplifier and tuneable laser in NIR band.

Formulation of Biocides Increases Antimicrobial Potency and Mitigates the Enrichment of Nonsusceptible Bacteria in Multispecies Biofilms

PubMed Central

Forbes, Sarah; Cowley, Nicola; Mistry, Hitesh; Amézquita, Alejandro

2017-01-01

ABSTRACT The current investigation aimed to generate data to inform the development of risk assessments of biocide usage. Stabilized domestic drain biofilm microcosms were exposed daily over 6 months to increasing concentrations (0.01% to 1%) of the biocide benzalkonium chloride (BAC) in a simple aqueous solution (BAC-s) or in a complex formulation (BAC-f) representative of a domestic cleaning agent. Biofilms were analyzed by culture, differentiating by bacterial functional group and by BAC or antibiotic susceptibility. Bacterial isolates were identified by 16S rRNA sequencing, and changes in biofilm composition were assessed by high-throughput sequencing. Exposure to BAC-f resulted in significantly larger reductions in levels of viable bacteria than exposure to BAC-s, while bacterial diversity greatly decreased during exposure to both BAC-s and BAC-f, as evidenced by sequencing and viable counts. Increases in the abundance of bacteria exhibiting reduced antibiotic or BAC susceptibility following exposure to BAC at 0.1% were significantly greater for BAC-s than BAC-f. Bacteria with reduced BAC and antibiotic susceptibility were generally suppressed by higher BAC concentrations, and formulation significantly enhanced this effect. Significant decreases in the antimicrobial susceptibility of bacteria isolated from the systems before and after long-term BAC exposure were not detected. In summary, dose-dependent suppression of bacterial viability by BAC was enhanced by formulation. Biocide exposure decreased bacterial diversity and transiently enriched populations of organisms with lower antimicrobial susceptibility, and the effects were subsequently suppressed by exposure to 1% BAC-f, the concentration most closely reflecting deployment in formulated products. IMPORTANCE Assessment of the risks of biocide use has been based mainly on the exposure of axenic cultures of bacteria to biocides in simple aqueous solutions. The current investigation aimed to assess the effects of formulation on the outcome of biocide exposure in multispecies biofilms. Formulation of the cationic biocide BAC significantly increased antimicrobial potency. Bacteria with lower antimicrobial susceptibility whose populations were enriched after low-level biocide exposure were more effectively suppressed by the biocide at in-use concentrations (1% [wt/vol]) in a formulation than in a simple aqueous solution. These observations underline the importance of simulating normal deployment conditions in considering the risks and benefits of biocide use. PMID:28115386

The association of alcohol-induced blackouts and grayouts to blood alcohol concentrations.

PubMed

Perry, Paul J; Argo, Tami R; Barnett, Mitchell J; Liesveld, Jill L; Liskow, Barry; Hernan, Jillian M; Trnka, Michael G; Brabson, Mary A

2006-07-01

The primary aim of this study was to investigate the association between measured blood alcohol concentration (BAC) and the presence and degree of amnesia (no amnesia, grayout, or blackout) in actively drinking subjects. A secondary aim was to determine potential factors other than BAC that contribute to the alcohol-induced memory loss. An interview questionnaire was administered to subjects regarding a recent alcohol associated arrest with a documented BAC greater than 0.08 g/dL for either public intoxication, driving under the influence, or under age drinking was administered. Demographic variables collected included drinking history, family history of alcoholism, presence of previous alcohol-related memory loss during a drinking episode, and drinking behavior during the episode. Memory of the drinking episode was evaluated to determine if either an alcohol-induced grayout (partial anterograde amnesia) or blackout (complete anterograde amnesia) occurred. Differences in (1) mean total number of drinks ingested before arrest, (2) gulping of drinks, and (3) BAC at arrest were found for those having blackouts compared with no amnesia; while differences in drinking more than planned were found between the no amnesia and grayout groups. A strong linear relationship between BAC and predicted probability of memory loss, particularly for blackouts was obvious. This finding clinically concludes that subjects with BAC of 310 g/dL or greater have a 0.50 or greater probability of having an alcoholic blackout.

Defining “Binge” Drinking as Five Drinks per Occasion or Drinking to a 0.08% BAC: Which is More Sensitive to Risk?

PubMed Central

Fillmore, Mark T.; Jude, Rebecca

2011-01-01

Heavy episodic or “binge” drinking is commonly defined as drinking 4–5 drinks per occasion (5/4 definition) or drinking that results in a blood alcohol concentration (BAC) of 0.08%. The present study compared the validity of each binge definition as an indicator of at-risk, problem drinking. 251 college students were classified as non-binge drinkers or as binge drinkers based on the 5/4 definition or the 0.08% BAC definition. The two definitions of binge drinking were examined in terms of their sensitivity and specificity as indicators of alcohol-related problems as determined by scores on the Alcohol Use Disorders Identification Test (AUDIT). Over half the sample (56%) were at-risk drinkers according to the AUDIT. The 0.08% definition detected only one-half of these individuals. Gender differences were also evident. Female binge drinkers actually achieved significantly higher estimated BACs per episode than their male binge drinking counterparts. The findings suggest that drinking to a sub-threshold BAC (i.e., < 0.08%) is not sufficient to avoid alcohol-related problems, and that total quantity (i.e., total standard drinks) per occasion might contribute to risk independent of the BAC achieved during drinking episodes. The findings also highlight the importance of considering frequency of consumption in determining risky drinking versus relying solely on quantity measures. PMID:21838847

Recombining overlapping BACs into a single larger BAC.

PubMed

Kotzamanis, George; Huxley, Clare

2004-01-06

BAC clones containing entire mammalian genes including all the transcribed region and long range controlling elements are very useful for functional analysis. Sequenced BACs are available for most of the human and mouse genomes and in many cases these contain intact genes. However, large genes often span more than one BAC, and single BACs covering the entire region of interest are not available. Here we describe a system for linking two or more overlapping BACs into a single clone by homologous recombination. The method was used to link a 61-kb insert carrying the final 5 exons of the human CFTR gene onto a 160-kb BAC carrying the first 22 exons. Two rounds of homologous recombination were carried out in the EL350 strain of bacteria which can be induced for the Red genes. In the first round, the inserts of the two overlapping BACs were subcloned into modified BAC vectors using homologous recombination. In the second round, the BAC to be added was linearised with the very rare-cutting enzyme I-PpoI and electroporated into recombination efficient EL350 bacteria carrying the other BAC. Recombined BACs were identified by antibiotic selection and PCR screening and 10% of clones contained the correctly recombined 220-kb BAC. The system can be used to link the inserts from any overlapping BAC or PAC clones. The original orientation of the inserts is not important and desired regions of the inserts can be selected. The size limit for the fragments recombined may be larger than the 61 kb used here and multiple BACs in a contig could be combined by alternating use of the two pBACLink vectors. This system should be of use to many investigators wishing to carry out functional analysis on large mammalian genes which are not available in single BAC clones.

Rapid CRISPR/Cas9-Mediated Cloning of Full-Length Epstein-Barr Virus Genomes from Latently Infected Cells.

PubMed

Yajima, Misako; Ikuta, Kazufumi; Kanda, Teru

2018-04-03

Herpesviruses have relatively large DNA genomes of more than 150 kb that are difficult to clone and sequence. Bacterial artificial chromosome (BAC) cloning of herpesvirus genomes is a powerful technique that greatly facilitates whole viral genome sequencing as well as functional characterization of reconstituted viruses. We describe recently invented technologies for rapid BAC cloning of herpesvirus genomes using CRISPR/Cas9-mediated homology-directed repair. We focus on recent BAC cloning techniques of Epstein-Barr virus (EBV) genomes and discuss the possible advantages of a CRISPR/Cas9-mediated strategy comparatively with precedent EBV-BAC cloning strategies. We also describe the design decisions of this technology as well as possible pitfalls and points to be improved in the future. The obtained EBV-BAC clones are subjected to long-read sequencing analysis to determine complete EBV genome sequence including repetitive regions. Rapid cloning and sequence determination of various EBV strains will greatly contribute to the understanding of their global geographical distribution. This technology can also be used to clone disease-associated EBV strains and test the hypothesis that they have special features that distinguish them from strains that infect asymptomatically.

Rapid CRISPR/Cas9-Mediated Cloning of Full-Length Epstein-Barr Virus Genomes from Latently Infected Cells

PubMed Central

Ikuta, Kazufumi; Kanda, Teru

2018-01-01

Herpesviruses have relatively large DNA genomes of more than 150 kb that are difficult to clone and sequence. Bacterial artificial chromosome (BAC) cloning of herpesvirus genomes is a powerful technique that greatly facilitates whole viral genome sequencing as well as functional characterization of reconstituted viruses. We describe recently invented technologies for rapid BAC cloning of herpesvirus genomes using CRISPR/Cas9-mediated homology-directed repair. We focus on recent BAC cloning techniques of Epstein-Barr virus (EBV) genomes and discuss the possible advantages of a CRISPR/Cas9-mediated strategy comparatively with precedent EBV-BAC cloning strategies. We also describe the design decisions of this technology as well as possible pitfalls and points to be improved in the future. The obtained EBV-BAC clones are subjected to long-read sequencing analysis to determine complete EBV genome sequence including repetitive regions. Rapid cloning and sequence determination of various EBV strains will greatly contribute to the understanding of their global geographical distribution. This technology can also be used to clone disease-associated EBV strains and test the hypothesis that they have special features that distinguish them from strains that infect asymptomatically. PMID:29614006

The Consequences of Providing Drinkers with Blood Alcohol Concentration Information on Assessments of Alcohol Impairment and Drunk-Driving Risk*

PubMed Central

JOHNSON, MARK B.; VOAS, ROBERT B.; KELLEY-BAKER, TARA; FURR-HOLDEN, C. DEBRA M.

2009-01-01

Objective We examined the effect of providing drinkers with blood alcohol concentration (BAC) information on subjective assessments of alcohol impairment and drunk-driving risk. Method We sampled 959 drinking participants from a natural drinking environment and asked them to self-administer a personal saliva-based alcohol test. Participants then were asked to rate their alcohol impairment and to indicate whether they could drive legally under one of four BAC feedback conditions (assigned at random): (1) control condition (no BAC feedback provided before the ratings); (2) categorical BAC information (low, high, and highest risk) from the saliva test; (3) categorical BAC information corroborated by a calibrated police breath alcohol analyzer; and (4) precise (three-digit) BAC information from the breath alcohol analyzer. Results Both control participants and participants who received precise BAC feedback gave subjective impairment ratings that correlated with actual BACs. For participants who received categorical BAC information from the saliva test, subjective impairment did not correlate with the actual BAC. Providing drinkers with BAC information, however, did help them predict more accurately if their BAC was higher than the legal BAC driving limit. Conclusions Although BAC information can influence drinkers’ assessments of alcohol impairment and drunk-driving risk, there is no strong evidence that personal saliva-based alcohol tests are particularly useful. PMID:18612570

Effects of Blood-Alcohol Concentration (BAC) Feedback on BAC Estimates Over Time

ERIC Educational Resources Information Center

Bullers, Susan; Ennis, Melissa

2006-01-01

This study examines the effects of self-tested blood alcohol concentration (BAC) feedback, from personal hand-held breathalyzers, on the accuracy of BAC estimation. Using an e-mail prompted web-based questionnaire, 19 participants were asked to report both BAC estimates and subsequently measured BAC levels over the course of 27 days. Results from…

The α-Effect and Competing Mechanisms: The Gas-Phase Reactions of Microsolvated Anions with Methyl Formate

NASA Astrophysics Data System (ADS)

Thomsen, Ditte L.; Nichols, Charles M.; Reece, Jennifer N.; Hammerum, Steen; Bierbaum, Veronica M.

2014-02-01

The enhanced reactivity of α-nucleophiles, which contain an electron lone pair adjacent to the reactive site, has been demonstrated in solution and in the gas phase and, recently, for the gas-phase SN2 reactions of the microsolvated HOO-(H2O) ion with methyl chloride. In the present work, we continue to explore the significance of microsolvation on the α-effect as we compare the gas-phase reactivity of the microsolvated α-nucleophile HOO-(H2O) with that of microsolvated normal alkoxy nucleophiles, RO-(H2O), in reactions with methyl formate, where three competing reactions are possible. The results reveal enhanced reactivity of HOO-(H2O) towards methyl formate, and clearly demonstrate the presence of an overall α-effect for the reactions of the microsolvated α-nucleophile. The association of the nucleophiles with a single water molecule significantly lowers the degree of proton abstraction and increases the SN2 and BAC2 reactivity compared with the unsolvated analogs. HOO-(H2O) reacts with methyl formate exclusively via the BAC2 channel. While microsolvation lowers the overall reaction efficiency, it enhances the BAC2 reaction efficiency for all anions compared with the unsolvated analogs. This may be explained by participation of the solvent water molecule in the BAC2 reaction in a way that continuously stabilizes the negative charge throughout the reaction.

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6.

PubMed

Szinay, Dóra; Chang, Song-Bin; Khrustaleva, Ludmila; Peters, Sander; Schijlen, Elio; Bai, Yuling; Stiekema, Willem J; van Ham, Roeland C H J; de Jong, Hans; Klein Lankhorst, René M

2008-11-01

Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.

College Students' Underestimation of Blood Alcohol Concentration from Hypothetical Consumption of Supersized Alcopops: Results from a Cluster-Randomized Classroom Study.

PubMed

Rossheim, Matthew E; Thombs, Dennis L; Krall, Jenna R; Jernigan, David H

2018-05-30

Supersized alcopops are a class of single-serving beverages popular among underage drinkers. These products contain large quantities of alcohol. This study examines the extent to which young adults recognize how intoxicated they would become from consuming these products. The study sample included 309 undergraduates who had consumed alcohol within the past year. Thirty-two sections of a college English course were randomized to 1 of 2 survey conditions, based on hypothetical consumption of supersized alcopops or beer of comparable liquid volume. Students were provided an empty can of 1 of the 2 beverages to help them answer the survey questions. Equation-calculated blood alcohol concentrations (BACs)-based on body weight and sex-were compared to the students' self-estimated BACs for consuming 1, 2, and 3 cans of the beverage provided to them. In adjusted regression models, students randomized to the supersized alcopop group greatly underestimated their BAC, whereas students randomized to the beer group overestimated it. The supersized alcopop group underestimated their BAC by 0.04 (95% confidence interval [CI]: 0.034, 0.053), 0.09 (95% CI: 0.067, 0.107), and 0.13 g/dl (95% CI: 0.097, 0.163) compared to the beer group. When asked how much alcohol they could consume before it would be unsafe to drive, students in the supersized alcopop group had 7 times the odds of estimating consumption that would generate a calculated BAC of at least 0.08 g/dl, compared to those making estimates based on beer consumption (95% CI: 3.734, 13.025). Students underestimated the intoxication they would experience from consuming supersized alcopops. Revised product warning labels are urgently needed to clearly identify the number of standard drinks contained in a supersized alcopop can. Moreover, regulations are needed to limit alcohol content of single-serving products. Copyright © 2018 by the Research Society on Alcoholism.

Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

PubMed Central

2010-01-01

Background The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy. Results The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries. Conclusions The negligibly low level of incorporation of clones from homoeologous chromosome arms into a contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes. PMID:20170511

Alcohol-related hospitalisations of trauma patients in Southern Taiwan: a cross-sectional study based on a trauma registry system

PubMed Central

Rau, Cheng-Shyuan; Liu, Hang-Tsung; Hsu, Shiun-Yuan; Cho, Tzu-Yu; Hsieh, Ching-Hua

2014-01-01

Objectives To provide an overview of the demographic characteristics of patients with positive blood alcohol concentration (BAC) and to investigate the performance of brain CT scans in these patients. Design Cross-sectional study. Setting Taiwan. Participants 2192 patients who had undergone a test for blood alcohol of 13 233 patients registered in the Trauma Registry System between 1 January 2009 and 31 December 2012. A BAC level of 50 mg/dL was defined as the cut-off value. Detailed information was retrieved from the patients with positive BAC (n=793) and was compared with information from those with a negative BAC (n=1399). Main outcome measures Glasgow Coma Scale (GCS) and Injury Severity Score (ISS) as well as the performance and findings of obtained brain CT scans. Results Patients with positive BAC had a higher rate of face injury, but a lower GCS score, a lower rate of head and neck injury, a lower ISS and New Injury Severity Score. Alcohol use was associated with a shorter length of hospital stay (8.6 vs 11.4 days, p=0.000) in patients with an ISS of <16. Of 496 patients with positive BAC who underwent brain CT, 164 (33.1%) showed positive findings on CT scan. In contrast, of 891 patients with negative BAC who underwent brain CT, 389 (43.7%) had positive findings on CT scan. The lower percentage of positive CT scan findings in patients with positive BAC was particularly evident in patients with an ISS <16 (18.0% vs 28.8%, p=0.001). Conclusions Patients who consumed alcohol tended to have a low GCS score and injuries that were less severe. However, given the significantly low percentage of positive findings, brain CT might be overused in these patients with less severe injuries. PMID:25361838

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

PubMed Central

Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.

2013-01-01

For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960

Combinatorial pooling enables selective sequencing of the barley gene space.

PubMed

Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J

2013-04-01

For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

Trophic effects of adipose-tissue-derived and bone-marrow-derived mesenchymal stem cells enhance cartilage generation by chondrocytes in co-culture

PubMed Central

Pleumeekers, M. M.; Nimeskern, L.; Koevoet, J. L. M.; Karperien, M.; Stok, K. S.; van Osch, G. J. V. M.

2018-01-01

Aims Combining mesenchymal stem cells (MSCs) and chondrocytes has great potential for cell-based cartilage repair. However, there is much debate regarding the mechanisms behind this concept. We aimed to clarify the mechanisms that lead to chondrogenesis (chondrocyte driven MSC-differentiation versus MSC driven chondroinduction) and whether their effect was dependent on MSC-origin. Therefore, chondrogenesis of human adipose-tissue-derived MSCs (hAMSCs) and bone-marrow-derived MSCs (hBMSCs) combined with bovine articular chondrocytes (bACs) was compared. Methods hAMSCs or hBMSCs were combined with bACs in alginate and cultured in vitro or implanted subcutaneously in mice. Cartilage formation was evaluated with biochemical, histological and biomechanical analyses. To further investigate the interactions between bACs and hMSCs, (1) co-culture, (2) pellet, (3) Transwell® and (4) conditioned media studies were conducted. Results The presence of hMSCs–either hAMSCs or hBMSCs—increased chondrogenesis in culture; deposition of GAG was most evidently enhanced in hBMSC/bACs. This effect was similar when hMSCs and bAC were combined in pellet culture, in alginate culture or when conditioned media of hMSCs were used on bAC. Species-specific gene-expression analyses demonstrated that aggrecan was expressed by bACs only, indicating a predominantly trophic role for hMSCs. Collagen-10-gene expression of bACs was not affected by hBMSCs, but slightly enhanced by hAMSCs. After in-vivo implantation, hAMSC/bACs and hBMSC/bACs had similar cartilage matrix production, both appeared stable and did not calcify. Conclusions This study demonstrates that replacing 80% of bACs by either hAMSCs or hBMSCs does not influence cartilage matrix production or stability. The remaining chondrocytes produce more matrix due to trophic factors produced by hMSCs. PMID:29489829

Trophic effects of adipose-tissue-derived and bone-marrow-derived mesenchymal stem cells enhance cartilage generation by chondrocytes in co-culture.

PubMed

Pleumeekers, M M; Nimeskern, L; Koevoet, J L M; Karperien, M; Stok, K S; van Osch, G J V M

2018-01-01

Combining mesenchymal stem cells (MSCs) and chondrocytes has great potential for cell-based cartilage repair. However, there is much debate regarding the mechanisms behind this concept. We aimed to clarify the mechanisms that lead to chondrogenesis (chondrocyte driven MSC-differentiation versus MSC driven chondroinduction) and whether their effect was dependent on MSC-origin. Therefore, chondrogenesis of human adipose-tissue-derived MSCs (hAMSCs) and bone-marrow-derived MSCs (hBMSCs) combined with bovine articular chondrocytes (bACs) was compared. hAMSCs or hBMSCs were combined with bACs in alginate and cultured in vitro or implanted subcutaneously in mice. Cartilage formation was evaluated with biochemical, histological and biomechanical analyses. To further investigate the interactions between bACs and hMSCs, (1) co-culture, (2) pellet, (3) Transwell® and (4) conditioned media studies were conducted. The presence of hMSCs-either hAMSCs or hBMSCs-increased chondrogenesis in culture; deposition of GAG was most evidently enhanced in hBMSC/bACs. This effect was similar when hMSCs and bAC were combined in pellet culture, in alginate culture or when conditioned media of hMSCs were used on bAC. Species-specific gene-expression analyses demonstrated that aggrecan was expressed by bACs only, indicating a predominantly trophic role for hMSCs. Collagen-10-gene expression of bACs was not affected by hBMSCs, but slightly enhanced by hAMSCs. After in-vivo implantation, hAMSC/bACs and hBMSC/bACs had similar cartilage matrix production, both appeared stable and did not calcify. This study demonstrates that replacing 80% of bACs by either hAMSCs or hBMSCs does not influence cartilage matrix production or stability. The remaining chondrocytes produce more matrix due to trophic factors produced by hMSCs.

Reducing false positives of microcalcification detection systems by removal of breast arterial calcifications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mordang, Jan-Jurre, E-mail: Jan-Jurre.Mordang@radboudumc.nl; Gubern-Mérida, Albert; Karssemeijer, Nico

Purpose: In the past decades, computer-aided detection (CADe) systems have been developed to aid screening radiologists in the detection of malignant microcalcifications. These systems are useful to avoid perceptual oversights and can increase the radiologists’ detection rate. However, due to the high number of false positives marked by these CADe systems, they are not yet suitable as an independent reader. Breast arterial calcifications (BACs) are one of the most frequent false positives marked by CADe systems. In this study, a method is proposed for the elimination of BACs as positive findings. Removal of these false positives will increase the performancemore » of the CADe system in finding malignant microcalcifications. Methods: A multistage method is proposed for the removal of BAC findings. The first stage consists of a microcalcification candidate selection, segmentation and grouping of the microcalcifications, and classification to remove obvious false positives. In the second stage, a case-based selection is applied where cases are selected which contain BACs. In the final stage, BACs are removed from the selected cases. The BACs removal stage consists of a GentleBoost classifier trained on microcalcification features describing their shape, topology, and texture. Additionally, novel features are introduced to discriminate BACs from other positive findings. Results: The CADe system was evaluated with and without BACs removal. Here, both systems were applied on a validation set containing 1088 cases of which 95 cases contained malignant microcalcifications. After bootstrapping, free-response receiver operating characteristics and receiver operating characteristics analyses were carried out. Performance between the two systems was compared at 0.98 and 0.95 specificity. At a specificity of 0.98, the sensitivity increased from 37% to 52% and the sensitivity increased from 62% up to 76% at a specificity of 0.95. Partial areas under the curve in the specificity range of 0.8–1.0 were significantly different between the system without BACs removal and the system with BACs removal, 0.129 ± 0.009 versus 0.144 ± 0.008 (p<0.05), respectively. Additionally, the sensitivity at one false positive per 50 cases and one false positive per 25 cases increased as well, 37% versus 51% (p<0.05) and 58% versus 67% (p<0.05) sensitivity, respectively. Additionally, the CADe system with BACs removal reduces the number of false positives per case by 29% on average. The same sensitivity at one false positive per 50 cases in the CADe system without BACs removal can be achieved at one false positive per 80 cases in the CADe system with BACs removal. Conclusions: By using dedicated algorithms to detect and remove breast arterial calcifications, the performance of CADe systems can be improved, in particular, at false positive rates representative for operating points used in screening.« less

Drinking and Driving in the United States: Comparing Results from the 2007 and 1996 National Roadside Surveys

PubMed Central

Kelley-Baker, Tara; Lacey, John H.; Voas, Robert B.; Romano, Eduardo; Yao, Jie; Berning, Amy

2013-01-01

Objectives The objectives of this study were to (a) use data from the 2007 National Roadside Survey (NRS) to determine the characteristics of weekend nighttime drivers with positive blood alcohol concentrations (BACs) on U.S. roads in 2007; (b) determine the relationship of the driving environment and trip characteristics associated with drinking drivers; and (c) compare the findings for the 2007 NRS with those for the 1996 NRS. Methods Like the 1996 NRS, the 2007 NRS used a stratified random national roadside survey sample of the contiguous 48 states and collected nighttime data on Fridays and Saturdays between 10 PM and 3 AM. Officers directed 8,384 drivers into off-road parking areas where our research team asked them to participate in the survey. Results Of those approached, 7,159 (85.4%) provided a breath test. Results revealed that 12% of the nighttime drivers had positive BACs, and of those, 2% were higher than the .08 BAC illegal limit in the United States. Since the 1996 NRS, we found significant reductions in the percentage of BAC-positive drivers across different demographic groups. Age was among the most significant factors associated with a weekend driver having a positive BAC. The probability that a driver would be drinking peaked in the 21- to 25-year-old age group. Male drivers were more likely than female drivers to be drinking, and Asian and Hispanic drivers were less likely than White drivers to be drinking. Drinking drivers were more likely to be driving short distances (5 or fewer miles), late at night (between 1 and 3 AM), and to be coming from a bar or restaurant. Finally, 26% of the drivers who reported that they would drive less than 5 miles on the night of the survey had positive BACs, compared to only 16% who indicated they would drive between 6 and 20 miles and 10% who planned to drive more than 20 miles. Conclusions The 2007 NRS provides another benchmark in the four-decade record of drinking drivers on American roads and provides a basis for measuring progress in combating driving under the influence during the coming decade. PMID:23343019

Genotype–phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21

PubMed Central

Lyle, Robert; Béna, Frédérique; Gagos, Sarantis; Gehrig, Corinne; Lopez, Gipsy; Schinzel, Albert; Lespinasse, James; Bottani, Armand; Dahoun, Sophie; Taine, Laurence; Doco-Fenzy, Martine; Cornillet-Lefèbvre, Pascale; Pelet, Anna; Lyonnet, Stanislas; Toutain, Annick; Colleaux, Laurence; Horst, Jürgen; Kennerknecht, Ingo; Wakamatsu, Nobuaki; Descartes, Maria; Franklin, Judy C; Florentin-Arar, Lina; Kitsiou, Sophia; Aït Yahya-Graison, Emilie; Costantine, Maher; Sinet, Pierre-Marie; Delabar, Jean M; Antonarakis, Stylianos E

2009-01-01

Down syndrome (DS) is one of the most frequent congenital birth defects, and the most common genetic cause of mental retardation. In most cases, DS results from the presence of an extra copy of chromosome 21. DS has a complex phenotype, and a major goal of DS research is to identify genotype–phenotype correlations. Cases of partial trisomy 21 and other HSA21 rearrangements associated with DS features could identify genomic regions associated with specific phenotypes. We have developed a BAC array spanning HSA21q and used array comparative genome hybridization (aCGH) to enable high-resolution mapping of pathogenic partial aneuploidies and unbalanced translocations involving HSA21. We report the identification and mapping of 30 pathogenic chromosomal aberrations of HSA21 consisting of 19 partial trisomies and 11 partial monosomies for different segments of HSA21. The breakpoints have been mapped to within ∼85 kb. The majority of the breakpoints (26 of 30) for the partial aneuploidies map within a 10-Mb region. Our data argue against a single DS critical region. We identify susceptibility regions for 25 phenotypes for DS and 27 regions for monosomy 21. However, most of these regions are still broad, and more cases are needed to narrow down the phenotypic maps to a reasonable number of candidate genomic elements per phenotype. PMID:19002211

Daily Associations Between Alcohol Consumption and Dating Violence Perpetration Among Men and Women: Effects of Self-Regulation

PubMed Central

Stappenbeck, Cynthia A.; Gulati, Natasha K.; Fromme, Kim

2016-01-01

Objective: Alcohol intoxication has been associated with dating violence perpetration, defined here as psychological and/or physical violence occurring between young adult dating partners. However, little is known about how the individual variability in the level of alcohol intoxication would influence dating violence perpetration and how sex and self-regulation might influence this association. Method: College-aged men and women (N = 146) from a large southwestern U.S. university completed background questionnaires, including the Brief Self-Control Scale, to assess self-regulation and then reported their dating violence perpetration and alcohol consumption using a 90-day Timeline Followback assessment. Their average estimated blood alcohol concentration (eBAC) and their daily deviation from this average were calculated for each of the 90 days to examine the between- and within-person effects of alcohol consumption, respectively. Results: Results of a two-level generalized estimating equation suggest that increases in daily eBAC were associated with an increased likelihood of perpetrating dating violence; however, this association was stronger for those who had a low average eBAC compared with those who had a high average eBAC. For those who had a low average eBAC, higher self-regulation was associated with a lower probability of perpetrating dating violence, whereas among those with a high average eBAC, self-regulation was not associated with dating violence perpetration. Sex did not moderate the association between eBAC and dating violence perpetration. Conclusions: Findings highlight the importance of self-regulation in dating violence perpetration—particularly for those with low average eBACs—and the need for varied intervention strategies, depending on one’s typical drinking pattern. PMID:26751365

Inhibition of ovarian cancer cell proliferation by a cell cycle inhibitory peptide fused to a thermally responsive polypeptide carrier.

PubMed

Massodi, Iqbal; Moktan, Shama; Rawat, Aruna; Bidwell, Gene L; Raucher, Drazen

2010-01-15

Current treatment of solid tumors is limited by normal tissue tolerance, resulting in a narrow therapeutic index. To increase drug specificity and efficacy and to reduce toxicity in normal tissues, we have developed a polypeptide carrier for a cell cycle inhibitory peptide, which has the potential to be thermally targeted to the tumor site. The design of this polypeptide is based on elastin-like polypeptide (ELP). The coding sequence of ELP was modified by the addition of the cell penetrating peptide Bac-7 at the N-terminus and a 23 amino acid peptide derived from p21 at the C-terminus (Bac-ELP1-p21). Bac-ELP1-p21 is soluble in aqueous solutions below physiological temperature (37 degrees C) but aggregates when the temperature is raised above 39 degrees C, making it a promising thermally responsive therapeutic carrier that may be actively targeted to solid tumors by application of focused hyperthermia. While Bac-ELP1-p21 at 37 degrees C did not have any effect on SKOV-3 cell proliferation, the use of hyperthermia increased the antiproliferative effect of Bac-ELP1-p21 compared with a thermally unresponsive control polypeptide. Bac-ELP1-p21 displayed both a cytoplasmic and nuclear distribution in the SKOV-3 cells, with nuclear-localized polypeptide enriched in the heated cells, as revealed by confocal microscopy. Using Western blotting, we show that Bac-ELP1-p21 caused a decrease in Rb phosphorylation levels in cells treated at 42 degrees C. The polypeptide also induced caspase activation, PARP cleavage, and cell cycle arrest in S-phase and G2/M-phase. These studies indicate that ELP is a promising macromolecular carrier for the delivery of cell cycle inhibitory peptides to solid tumors.

Does alcohol intoxication protect patients from severe injury and reduce hospital mortality? The association of alcohol consumption with the severity of injury and survival in trauma patients.

PubMed

Hsieh, Chi-Hsun; Su, Li-Ting; Wang, Yu-Chun; Fu, Chih-Yuan; Lo, Hung-Chieh; Lin, Chiu-Hsiu

2013-12-01

Alcohol-related motor vehicle collisions are a major cause of mortality in trauma patients. This prospective observational study investigated the influence of antecedent alcohol use on outcomes in trauma patients who survived to reach the hospital. From 2005 to 2011, all patients who were older than 18 years and were admitted as a result of motor vehicle crashes were included. Blood alcohol concentration (BAC) was routinely measured for each patient on admission. Patients were divided into four groups based on their BAC level, which included nondrinking, BAC less than 100, BAC 100 to 200, and BAC 200 mg/dL or greater. Patient demographics, physical status and injury severity on admission, length of hospital stay, and outcome were compared between the groups. Odds ratios of having a severe injury, prolonged hospital stay, and mortality were estimated. Patients with a positive BAC had an increased risk of sustaining craniofacial and thoracoabdominal injuries. Odds ratios of having severe injuries (Injury Severity Score [ISS] 16 or greater) and a prolonged hospital stay were also increased. However, for those patients whose ISS was 16 or greater and who also had a brain injury, risk of fatality was significantly reduced if they were intoxicated (BAC 200 mg/dL or greater) before injury. Alcohol consumption does not protect patients from sustaining severe injuries nor does it shorten the length of hospital stay. However, there were potential survival benefits related to alcohol consumption for patients with brain injuries but not for those without brain injuries. Additional research is required to investigate the mechanism of this association further.

“Let’s get Wasted!” and Other Apps: Characteristics, Acceptability, and Use of Alcohol-Related Smartphone Applications

PubMed Central

Weaver, Emma R; Horyniak, Danielle R; Jenkinson, Rebecca; Dietze, Paul

2013-01-01

Background Smartphone applications (“apps”) offer a number of possibilities for health promotion activities. However, young people may also be exposed to apps with incorrect or poor quality information, since, like the Internet, apps are mostly unregulated. Little is known about the quality of alcohol-related apps or what influence they may have on young people’s behavior. Objective To critically review popular alcohol-related smartphone apps and to explore young people’s opinions of these apps, their acceptability, and use for alcohol-related health promotion. Methods First, a content analysis of 500 smartphone apps available via Apple iTunes and Android Google Play stores was conducted. Second, all available blood alcohol concentration (BAC) apps were tested against four individual case profiles of known BAC from a previous study. Third, two focus group discussions explored how young people use alcohol-related apps, particularly BAC apps. Results 384 apps were included; 50% (192) were entertainment apps, 39% (148) were BAC apps, and 11% (44) were health promotion and/or stop drinking–related apps. When testing the BAC apps, there was wide variation in results, with apps tending to overestimate BAC scores compared with recorded scores. Participants were skeptical of the accuracy of BAC apps, and there was an overall concern that these apps would be used as a form of entertainment, further encouraging young people to drink, rather than reduce their drinking and risk taking. Conclusions The majority of popular alcohol-related apps encouraged alcohol consumption. Apps estimating blood alcohol concentration were widely available but were highly unreliable. Health departments and prominent health organizations need to endorse alcohol smartphone apps that are accurate and evidence-based to give specific apps credibility in the ever-expanding market of unregulated apps. PMID:25100681

Influence of dissolved oxygen concentration on the pharmacokinetics of alcohol in humans.

PubMed

Baek, In-hwan; Lee, Byung-yo; Kwon, Kwang-il

2010-05-01

Ethanol oxidation by the microsomal ethanol oxidizing system requires oxygen for alcohol metabolism, and a higher oxygen uptake increases the rate of ethanol oxidation. We investigated the effect of dissolved oxygen on the pharmacokinetics of alcohol in healthy humans (n = 49). The concentrations of dissolved oxygen were 8, 20, and 25 ppm in alcoholic drinks of 240 and 360 ml (19.5% v/v). Blood alcohol concentrations (BACs) were determined by converting breath alcohol concentrations. Breath samples were collected every 30 min when the BAC was higher than 0.015%, 20 min at BAC < or =0.015%, 10 min at BAC < or =0.010%, and 5 min at BAC < or =0.006%. The high dissolved oxygen groups (20, 25 ppm) descended to 0.000% and 0.050% BAC faster than the normal dissolved oxygen groups (8 ppm; p < 0.05). In analyzing pharmacokinetic parameters, AUC(inf) and K(el) of the high oxygen groups were lower than in the normal oxygen group, while C(max) and T(max) were not significantly affected. In a Monte Carlo simulation, the lognormal distribution of mean values of AUC(inf) and t(1/2) was expected to be reduced in the high oxygen group compared to the normal oxygen group. In conclusion, elevated dissolved oxygen concentrations in alcoholic drinks accelerate the metabolism and elimination of alcohol. Thus, enhanced dissolved oxygen concentrations in alcohol may have a role to play in reducing alcohol-related side effects and accidents.

Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

PubMed Central

Liu, Changqing; Bai, Chunyu; Guo, Yu; Liu, Dan; Lu, Taofeng; Li, Xiangchen; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

2014-01-01

Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger. PMID:24608928

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.

PubMed

Haiminen, Niina; Feltus, F Alex; Parida, Laxmi

2011-04-15

We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using in silico simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence. The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on Arabidopsis. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most. BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.

Outcomes and resource utilization associated with underage drinking at a level I trauma center.

PubMed

Psoter, Kevin J; Roudsari, Bahman S; Mack, Christopher; Vavilala, Monica S; Jarvik, Jeffrey G

2014-08-01

To examine the association of blood alcohol content (BAC) on hospital-based outcomes and imaging utilization for patients <21 years admitted to a level I trauma center. Retrospective analysis of alcohol-involved injuries in patients 13-20 years, admitted to a level I trauma center from 1996 to 2010. An injury was considered alcohol involved if the patient had a BAC > 0. Multivariable logistic regression was used to compare mortality, discharge destination (home and skilled nursing facility), intensive care unit admission, and operating room use between patients with and without positive BAC for patients 13-15, 16-17, and 18-20 years. Multivariable linear regression was used to compare length of hospitalization. Finally, multivariable negative binomial regression evaluated radiology resource utilization (x-ray, computed tomography [CT], and magnetic resonance imaging). A total of 7,663 patients, 13-20 years old, were admitted over the study period. A positive BAC was reported in 19% of these patients. In general, the presence of alcohol was not associated with mortality rate, length of hospitalization, intensive care unit, and operating room use or discharge status for any age group. However, the presence of alcohol was associated with higher utilization of head (incidence rate ratio [IRR] 1.13, 95% confidence interval [CI] 1.02-1.26), cervical spine (IRR 1.10, 95% CI 1.01-1.22), and thoracic (IRR 1.30, 95% CI 1.05-1.63) CTs in young adults 18-20 years. No differences in CT use were observed in patients 13-15 or 16-17 years. Positive BAC was not significantly associated with adverse outcomes or resource utilization in younger trauma patients. However, the use of certain body region CTs was associated with positive BAC in patients 18-20 years. Copyright © 2014 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments.

PubMed

Chen, Chao; Zhao, Xinqing; Jin, Yingyu; Zhao, Zongbao Kent; Suh, Joo-Won

2014-11-01

Bacterial artificial chromosomal (BAC) vectors are increasingly being used in cloning large DNA fragments containing complex biosynthetic pathways to facilitate heterologous production of microbial metabolites for drug development. To express inserted genes using Streptomyces species as the production hosts, an integration expression cassette is required to be inserted into the BAC vector, which includes genetic elements encoding a phage-specific attachment site, an integrase, an origin of transfer, a selection marker and a promoter. Due to the large sizes of DNA inserted into the BAC vectors, it is normally inefficient and time-consuming to assemble these fragments by routine PCR amplifications and restriction-ligations. Here we present a rapid method to insert fragments to construct BAC-based expression vectors. A DNA fragment of about 130 bp was designed, which contains upstream and downstream homologous sequences of both BAC vector and pIB139 plasmid carrying the whole integration expression cassette. In-Fusion cloning was performed using the designer DNA fragment to modify pIB139, followed by λ-RED-mediated recombination to obtain the BAC-based expression vector. We demonstrated the effectiveness of this method by rapid construction of a BAC-based expression vector with an insert of about 120 kb that contains the entire gene cluster for biosynthesis of immunosuppressant FK506. The empty BAC-based expression vector constructed in this study can be conveniently used for construction of BAC libraries using either microbial pure culture or environmental DNA, and the selected BAC clones can be directly used for heterologous expression. Alternatively, if a BAC library has already been constructed using a commercial BAC vector, the selected BAC vectors can be manipulated using the method described here to get the BAC-based expression vectors with desired gene clusters for heterologous expression. The rapid construction of a BAC-based expression vector facilitates heterologous expression of large gene clusters for drug discovery. Copyright © 2014 Elsevier Inc. All rights reserved.

Evaluating wait times from screening to breast cancer diagnosis among women undergoing organised assessment vs usual care

PubMed Central

Chiarelli, Anna M; Muradali, Derek; Blackmore, Kristina M; Smith, Courtney R; Mirea, Lucia; Majpruz, Vicky; O'Malley, Frances P; Quan, May Lynn; Holloway, Claire MB

2017-01-01

Background: Timely coordinated diagnostic assessment following an abnormal screening mammogram reduces patient anxiety and may optimise breast cancer prognosis. Since 1998, the Ontario Breast Screening Program (OBSP) has offered organised assessment through Breast Assessment Centres (BACs). For OBSP women seen at a BAC, an abnormal mammogram is followed by coordinated referrals through the use of navigators for further imaging, biopsy, and surgical consultation as indicated. For OBSP women seen through usual care (UC), further diagnostic imaging is arranged directly from the screening centre and/or through their physician; results must be communicated to the physician who is then responsible for arranging any necessary biopsy and/or surgical consultation. This study aims to evaluate factors associated with diagnostic wait times for women undergoing assessment through BAC and UC. Methods: Of the 2 147 257 women aged 50–69 years screened in the OBSP between 1 January 2002 and 31 December 2009, 155 866 (7.3%) had an abnormal mammogram. A retrospective design identified two concurrent cohorts of women diagnosed with screen-detected breast cancer at a BAC (n=4217; 47%) and UC (n=4827; 53%). Multivariable logistic regression analyses examined associations between wait times and assessment and prognostic characteristics by pathway. A two-sided 5% significance level was used. Results: Screened women with breast cancer were two times more likely to be diagnosed within 7 weeks when assessed through a BAC vs UC (OR=1.91, 95% CI=1.73–2.10). In addition, compared with UC, women assessed through a BAC were significantly more likely to have their first assessment procedure within 3 weeks of their abnormal mammogram (OR=1.25, 95% CI=1.12–1.39), ⩽3 assessment procedures (OR=1.54, 95% CI=1.41–1.69), ⩽2 assessment visits (OR=1.86, 95% CI=1.70–2.05), and ⩾2 procedures per visit (OR=1.41, 95% CI=1.28–1.55). Women diagnosed through a BAC were also more likely than those in UC to have imaging (OR=1.99, 95% CI=1.44–2.75) or a biopsy (OR=3.69, 95% CI=2.64–5.15) vs consultation only at their first assessment visit, and two times more likely to have a core or FNA biopsy than a surgical biopsy (OR=2.08, 95% CI=1.81–2.40). Having ⩽2 assessment visits was more likely to reduce time to diagnosis for women assessed through a BAC compared with UC (BAC OR=10.58, 95% CI=8.96–12.50; UC OR=4.47, 95% CI=3.94–5.07), as was having ⩽3 assessment procedures (BAC OR=4.97, 95% CI=4.26–5.79; UC OR=2.95, 95% CI=2.61–3.33). Income quintile affected wait times only in women diagnosed in UC, with those in the two highest quintiles more likely to receive a diagnosis in 7 weeks. Conclusions: Women with screen-detected breast cancer in OBSP were more likely to have shorter wait times if they were diagnosed through organised assessment. This might be as a result of women diagnosed through a BAC having more procedures per visit, procedures scheduled in shorter intervals, and imaging or biopsy on their first visit. Given the significant improvement in timeliness to diagnosis, women with abnormal mammograms should be managed through organised assessment. PMID:28359079

Evaluating wait times from screening to breast cancer diagnosis among women undergoing organised assessment vs usual care.

PubMed

Chiarelli, Anna M; Muradali, Derek; Blackmore, Kristina M; Smith, Courtney R; Mirea, Lucia; Majpruz, Vicky; O'Malley, Frances P; Quan, May Lynn; Holloway, Claire Mb

2017-05-09

Timely coordinated diagnostic assessment following an abnormal screening mammogram reduces patient anxiety and may optimise breast cancer prognosis. Since 1998, the Ontario Breast Screening Program (OBSP) has offered organised assessment through Breast Assessment Centres (BACs). For OBSP women seen at a BAC, an abnormal mammogram is followed by coordinated referrals through the use of navigators for further imaging, biopsy, and surgical consultation as indicated. For OBSP women seen through usual care (UC), further diagnostic imaging is arranged directly from the screening centre and/or through their physician; results must be communicated to the physician who is then responsible for arranging any necessary biopsy and/or surgical consultation. This study aims to evaluate factors associated with diagnostic wait times for women undergoing assessment through BAC and UC. Of the 2 147 257 women aged 50-69 years screened in the OBSP between 1 January 2002 and 31 December 2009, 155 866 (7.3%) had an abnormal mammogram. A retrospective design identified two concurrent cohorts of women diagnosed with screen-detected breast cancer at a BAC (n=4217; 47%) and UC (n=4827; 53%). Multivariable logistic regression analyses examined associations between wait times and assessment and prognostic characteristics by pathway. A two-sided 5% significance level was used. Screened women with breast cancer were two times more likely to be diagnosed within 7 weeks when assessed through a BAC vs UC (OR=1.91, 95% CI=1.73-2.10). In addition, compared with UC, women assessed through a BAC were significantly more likely to have their first assessment procedure within 3 weeks of their abnormal mammogram (OR=1.25, 95% CI=1.12-1.39), ⩽3 assessment procedures (OR=1.54, 95% CI=1.41-1.69), ⩽2 assessment visits (OR=1.86, 95% CI=1.70-2.05), and ⩾2 procedures per visit (OR=1.41, 95% CI=1.28-1.55). Women diagnosed through a BAC were also more likely than those in UC to have imaging (OR=1.99, 95% CI=1.44-2.75) or a biopsy (OR=3.69, 95% CI=2.64-5.15) vs consultation only at their first assessment visit, and two times more likely to have a core or FNA biopsy than a surgical biopsy (OR=2.08, 95% CI=1.81-2.40). Having ⩽2 assessment visits was more likely to reduce time to diagnosis for women assessed through a BAC compared with UC (BAC OR=10.58, 95% CI=8.96-12.50; UC OR=4.47, 95% CI=3.94-5.07), as was having ⩽3 assessment procedures (BAC OR=4.97, 95% CI=4.26-5.79; UC OR=2.95, 95% CI=2.61-3.33). Income quintile affected wait times only in women diagnosed in UC, with those in the two highest quintiles more likely to receive a diagnosis in 7 weeks. Women with screen-detected breast cancer in OBSP were more likely to have shorter wait times if they were diagnosed through organised assessment. This might be as a result of women diagnosed through a BAC having more procedures per visit, procedures scheduled in shorter intervals, and imaging or biopsy on their first visit. Given the significant improvement in timeliness to diagnosis, women with abnormal mammograms should be managed through organised assessment.

Transformation of benzalkonium chloride under nitrate reducing conditions.

PubMed

Tezel, Ulas; Pavlostathis, Spyros G

2009-03-01

The effect and transformation potential of benzalkonium chlorides (BAC) under nitrate reducing conditions were investigated at concentrations up to 100 mg/L in batch assays using a mixed, mesophilic (35 degrees C) methanogenic culture. Glucose was used as the carbon and energy source and the initial nitrate concentration was 70 mg N/L Dissimilatory nitrate reduction to ammonia (DNRA) and to dinitrogen (DNRN) were observed at BAC concentrations up to 25 mg/L At and above 50 mg BAC/L, DNRA was inhibited and DNRN was incomplete resulting in accumulation of nitrous oxide. Long-term inhibition of methanogenesis and accumulation of volatile fatty acids were observed at and above 50 mg BAC/L Over 99% of the added BAC was recovered from all cultures except the one amended with 100 mg BAC/L where 37% of the initially added BAC was transformed during the 100 day incubation period. Abiotic and biotic assays performed with 100 mg/L of BAC and 5 mM (in the liquid phase) of either nitrate, nitrite, or nitric oxide demonstrated that BAC transformation was abiotic and followed the modified Hofmann degradation pathway, i.e., bimolecular nucleophilic substitution with nitrite. Alkyl dimethyl amines (tertiary amines) were produced at equamolar levels to BAC transformed, but were not further degraded. This is the first report demonstrating the transformation of BAC under nitrate reducing conditions and elucidating the BAC transformation pathway.

Time-to-detection of bacteria and yeast with the BACTEC FX versus BacT/Alert Virtuo blood culture systems.

PubMed

Somily, Ali Mohammed; Habib, Hanan Ahmed; Torchyan, Armen Albert; Sayyed, Samina B; Absar, Muhammed; Al-Aqeel, Rima; Binkhamis, A Khalifa

2018-01-01

Bloodstream infections are associated with high rates of morbidity and mortality. Rapid detection of bloodstream infections is important in achieving better patient outcomes. Compare the time-to-detection (TTD) of the new BacT/Alert Virtuo and the BACTEC FX automated blood culture systems. Prospective simulated comparison of two instruments using seeded samples. Medical microbiology laboratory. Blood culture bottles were seeded in triplicate with each of the standard ATCC strains of aerobes, anaerobes and yeast. TTD was calculated as the length of time from the beginning of culture incubation to the detection of bacterial growth. TTD for the various tested organisms on the two microbial detection systems. The 99 bottles of seeded blood cultures incubated in each of the blood culture systems included 21 anaerobic, 39 aerobic and 39 pediatric bottles. The BacT/Alert Virtuo system exhibited significantly shorter TTD for 72.7 % of the tested organisms compared to BACTEC FX system with a median difference in mean TTD of 2.1 hours (interquartile range: 1.5-3.5 hours). The BACTEC FX system was faster in 15.2% (5/33) of microorganisms, with a median difference in mean TTD of 25.9 hours (IQR: 9.1-29.2 hours). TTD was significantly shorter for most of the microorganisms tested on the new BacT/Alert Virtuo system compared to the BACTEC FX system. Use of simulated cultures to assess TTD may not precisely represent clinical blood cultures. None.

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

PubMed

Perera, Dinum; Magbanua, Zenaida V; Thummasuwan, Supaphan; Mukherjee, Dipaloke; Arick, Mark; Chouvarine, Philippe; Nairn, Campbell J; Schmutz, Jeremy; Grimwood, Jane; Dean, Jeffrey F D; Peterson, Daniel G

2018-07-15

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Features of the organization of bread wheat chromosome 5BS based on physical mapping.

PubMed

Salina, Elena A; Nesterov, Mikhail A; Frenkel, Zeev; Kiseleva, Antonina A; Timonova, Ekaterina M; Magni, Federica; Vrána, Jan; Šafář, Jan; Šimková, Hana; Doležel, Jaroslav; Korol, Abraham; Sergeeva, Ekaterina M

2018-02-09

The IWGSC strategy for construction of the reference sequence of the bread wheat genome is based on first obtaining physical maps of the individual chromosomes. Our aim is to develop and use the physical map for analysis of the organization of the short arm of wheat chromosome 5B (5BS) which bears a number of agronomically important genes, including genes conferring resistance to fungal diseases. A physical map of the 5BS arm (290 Mbp) was constructed using restriction fingerprinting and LTC software for contig assembly of 43,776 BAC clones. The resulting physical map covered ~ 99% of the 5BS chromosome arm (111 scaffolds, N50 = 3.078 Mb). SSR, ISBP and zipper markers were employed for anchoring the BAC clones, and from these 722 novel markers were developed based on previously obtained data from partial sequencing of 5BS. The markers were mapped using a set of Chinese Spring (CS) deletion lines, and F2 and RICL populations from a cross of CS and CS-5B dicoccoides. Three approaches have been used for anchoring BAC contigs on the 5BS chromosome, including clone-by-clone screening of BACs, GenomeZipper analysis, and comparison of BAC-fingerprints with in silico fingerprinting of 5B pseudomolecules of T. dicoccoides. These approaches allowed us to reach a high level of BAC contig anchoring: 96% of 5BS BAC contigs were located on 5BS. An interesting pattern was revealed in the distribution of contigs along the chromosome. Short contigs (200-999 kb) containing markers for the regions interrupted by tandem repeats, were mainly localized to the 5BS subtelomeric block; whereas the distribution of larger 1000-3500 kb contigs along the chromosome better correlated with the distribution of the regions syntenic to rice, Brachypodium, and sorghum, as detected by the Zipper approach. The high fingerprinting quality, LTC software and large number of BAC clones selected by the informative markers in screening of the 43,776 clones allowed us to significantly increase the BAC scaffold length when compared with the published physical maps for other wheat chromosomes. The genetic and bioinformatics resources developed in this study provide new possibilities for exploring chromosome organization and for breeding applications.

The Diagnostic Utility of Bact/ALERT and Nested PCR in the Diagnosis of Tuberculous Meningitis.

PubMed

Sastry, Apurba Sankar; Bhat K, Sandhya; Kumudavathi

2013-01-01

The early laboratory diagnosis of Tuberculous Meningitis (TBM) is crucial, to start the antitubercular chemotherapy and to prevent its complications. However, the conventional methods are either less sensitive or time consuming. Hence, the diagnostic potentials of BacT/ALERT and Polymerase Chain Reaction (PCR) was evaluated in this study. The study group comprised of 62 cases and 33 controls. The cases were divided according to Ahuja's criteria into the confirmed (two cases), highly probable (19 cases), probable (26 cases) and the possible (15 cases) subgroups. Ziehl Neelsen's (ZN) and Auramine Phenol (AP) staining, Lowenstein Jensen (LJ) medium culture, BacT/ALERT and nested Polymerase Chain Reaction (PCR) which targeted IS6110 were carried out on all the patients. The sensitivity of the LJ culture was 3.22%. BacT/ALERT showed a sensitivity and a specificity of 25.80% and 100% and those of nested PCR were found to be 40.32% and 96.97% respectively. The mean detection time of growth of the LJ culture was 31.28 days, whereas that of BacT/ALERT was 20.68 days. The contamination rate in the LJ culture and BacT/ALERT were 7.2% and 5.8% respectively. Nested PCR was found to be more sensitive, followed by BacT/ALERT as compared to the LJ culture and smear microscopy. As both false negative and false positive results have been reported for nested PCR, so it should not be used alone as a criterion for initiating or terminating the therapy, but it should be supported by clinical, radiological, cytological and other microbiological findings.

Catecholamine levels in the brain of rats exposed by inhalation to benzalkonium chloride.

PubMed

Swiercz, Radosław; Grzelińska, Zofia; Gralewicz, Sławomir; Wasowicz, Wojciech

2009-01-01

The aim of the study was to obtain quantitative data on the effect of inhalation exposure to benzalkonium chloride (BAC) on the concentration of catecholamines and their metabolites in selected brain structures. Additionally, concentration of corticosterone (CORT) in plasma was estimated. Wistar rats were subjected to a single (6-hour) or repeated (3 days, 6 h/day) exposure to BAC aerosol at ca. 30 mg/m3. The Waters integrated analytical system of HPLC was used to determine the plasma corticosterone. Qualitative and quantitative determinations of catecholamines and their metabolites: 3,4-dihydroxyphenylacetic (DOPAC) and homovanillic (HVA) acids were performed with the use of the Waters integrity HPLC. The determinations have shown that in the BAC-exposed rats the plasma CORT concentration was several times higher than in the control rats. A significant increase of the concentration of dopamine (DA) (striatum and diencephalon) and noradrenaline (NA) (hippocampus and cerebellum) and a significant reduction of adrenaline (A) level (cortex, hippocampus, striatum and mesencephaloon) was found to occur in the brain of rats exposed to BAC compared to control. In the animals exposed to BAC, the concentration of DOPAC, a DA metabolite, was significantly reduced, but the change occurred mainly in the striatum. This resulted in a significant decrease of the DOPAC/DA and HVA/DA metabolic ratio in this structure. It is assumed that the alterations in the concentration of catecholamines and their metabolites in the BAC-exposed rats were related to the unexpectedly strong and persistent activation of the hypothalamo-pituitary-adrenocortical (HPA) axis evidenced by the high plasma CORT concentration.

A Comparison of the Effects of Benzalkonium Chloride on Ocular Surfaces between C57BL/6 and BALB/c Mice

PubMed Central

Yang, Qian; Zhang, Yafang; Liu, Xiuping; Wang, Nan; Song, Zhenyu; Wu, Kaili

2017-01-01

Models of benzalkonium chloride (BAC)-induced ocular disruption have been created and are widely used in various animals. This study aimed to compare the effects of BAC on the ocular surfaces of C57BL/6 and BALB/c mice. C57BL/6 and BALB/c mice were treated separately with BAC eye-drops at different concentrations. Eyes were evaluated by scoring epithelial disruption, corneal opacity and neovascularization in vivo, and by histological assays with hematoxylin/eosin (H/E) and periodic acid-Schiff stainings and by determining the expression of inflammatory factors in vitro on Days 7 and 14. The in vivo corneal epithelial disruption, corneal edema/opacity and neovascularization, which were in accordance with the results of the H/E staining and peaked at Day 7, were observed in a dose-dependent manner in the BAC-treated mice, with more severe signs in the C57BL/6 mice than the BALB/c mice. The loss of conjunctival goblet cells in the conjunctivas and the increasing expression of monocyte chemoattractant protein 1 (MCP-1), growth-regulated protein alpha (GROa) and macrophage inflammatory protein-1 alpha (MIP-1a) in the corneas were found in a dose-dependent manner in both strains of mice. Topical application of BAC can dramatically disrupt the ocular surfaces of C57BL/6 and BALB/c mice, and the disruptions were much more severe in the C57BL/6 mice that received high doses of BAC. PMID:28245636

Study I: effects of 0.06% and 0.10% blood alcohol concentration on human postural control.

PubMed

Modig, F; Patel, M; Magnusson, M; Fransson, P A

2012-03-01

Alcohol intoxication causes many accidental falls presented at emergency departments, with the injury severity often related to level of blood alcohol concentration (BAC). One way to evaluate the decline in postural control and the fall risk is to assess standing stability when challenged. The study objective was to comprehensively investigate alcohol-related impairments on postural control and adaptive motor learning at specific BAC levels. Effects of alcohol intoxication at 0.06% and 0.10% BAC were examined with posturography when unperturbed or perturbed by calf vibration. Twenty-five participants (mean age 25.1 years) were investigated standing with either eyes open or closed. Our results revealed several significant findings: (1) stability declined much faster from alcohol intoxication between 0.06% and 0.10% BAC (60-140%) compared with between 0.0% and 0.06% BAC (30%); (2) sustained exposure to repeated balance perturbations augmented the alcohol-related destabilization; (3) there were stronger effects of alcohol intoxication on stability in lateral direction than in anteroposterior direction; and (4) there was a gradual degradation of postural control particularly in lateral direction when the balance perturbations were repeated at 0.06% and 0.10% BAC, indicating adaptation deficits when intoxicated. To summarize, alcohol has profound deteriorating effects on human postural control, which are dose dependent, time dependent and direction specific. The maximal effects of alcohol intoxication on physiological performance might not be evident initially, but may be revealed first when under sustained sensory-motor challenges. Copyright © 2011 Elsevier B.V. All rights reserved.

Genomic and transcriptomic insights into how bacteria withstand high concentrations of benzalkonium chloride biocides.

PubMed

Kim, Minjae; Hatt, Janet K; Weigand, Michael R; Krishnan, Raj; Pavlostathis, Spyros G; Konstantinidis, Konstantinos T

2018-04-13

Benzalkonium chlorides (BAC) are commonly used biocides in broad-spectrum disinfectant solutions. How microorganisms cope with BAC exposure remains poorly understood, despite its importance for disinfection and disinfectant-induced antibiotic resistance. To provide insights into these issues, we exposed two isolates of an opportunistic pathogen, Pseudomonas aeruginosa , to increasing concentrations of BAC. One isolate was pre-adapted to BAC as it originated from a bioreactor fed with sub-inhibitory concentrations of BAC for 3 years, while the other originated from a bioreactor that received no BAC. Replicated populations of both isolates were able to survive high concentrations of BAC, up to 1200 and 1600mg/L for the non- and pre-adapted ones, respectively, exceeding typical application doses. RNA-seq analysis revealed up-regulation of efflux pump genes and decreased expression of porins related to BAC transport as well as reduced growth rate. Increased expression of spermidine (a polycation) synthase genes and mutations in the pmrB (polymyxin resistance) gene, which cause a reduction in membrane negative charge, suggested that a major adaptation to exposure to the cationic surfactant BAC was to actively stabilize cell surface charge. Collectively, these results revealed that P. aeruginosa adapts to BAC exposure by a combination of mechanisms, and provided genetic markers to monitor BAC-resistant organisms that may have applications in the practice of disinfection. Importance Benzalkonium chlorides (BAC) are widely used as biocides in disinfectant solutions, food processing lines, domestic households, and healthcare facilities. Due to their wide use and mode of action, there has been rising concern that BAC may promote antibiotic resistance. Consistently, at least 40 outbreaks have been attributed to infection by disinfectant- and antibiotic-resistant pathogens such as Pseudomonas aeruginosa However, the underlying molecular mechanisms that bacteria deal with BAC exposure remain poorly elucidated. Elucidating these mechanisms may be important for monitoring and limiting the spreading of disinfectant-resistant pathogens. Using an integrated approach that combined genomics and transcriptomics with physiological characterization of BAC-adapted isolates, this study provided a comprehensive understanding of the BAC-resistance mechanisms in P. aeruginosa Our findings also revealed potential genetic markers to detect and monitor the abundance of BAC-resistant pathogens across clinical or environmental settings. Copyright © 2018 American Society for Microbiology.

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

PubMed Central

2011-01-01

Background We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using in silico simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence. Results The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on Arabidopsis. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most. Conclusions BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies. PMID:21496274

BacMam virus-based surface display of the infectious bronchitis virus (IBV) S1 glycoprotein confers strong protection against virulent IBV challenge in chickens.

PubMed

Zhang, Jie; Chen, Xiao-Wei; Tong, Tie-Zhu; Ye, Yu; Liao, Ming; Fan, Hui-Ying

2014-02-03

Avian infectious bronchitis virus (IBV) is associated with production inefficiencies in domestic fowl, and causes massive economic losses to the poultry industry worldwide. Progress has been made in designing novel and efficient candidate vaccines to control IBV infection. BacMam virus, a modified baculovirus mediating transgene expression under the control of a mammalian promoter, has emerged as a versatile and safe vector during vaccine development. In previous work, we generated the BacMam virus Ac-CMV-S1, which expressed the S1 glycoprotein of IBV-M41. We showed that Ac-CMV-S1 induced excellent cellular immunity, but did not confer adequate protection in chickens compared with the conventional inactivated vaccine. In the current study, we generated an improved BacMam virus, BV-Dual-S1. This virus displayed the S1 glycoprotein on the baculovirus envelope, and was capable of expressing it in mammalian cells. BV-Dual-S1 elicited stronger humoral and cell-mediated immune responses, and showed greater capacity for induction of cytotoxic T lymphocyte responses, compared with Ac-CMV-S1 in specific pathogen-free chickens. A significant difference was not observed for protection rates between chickens immunized with BV-Dual-S1 (83%) or inactivated vaccine (89%) following challenge with virulent IBV-M41. Our findings show that the protective efficacy of BV-Dual-S1 could be significantly enhanced by baculovirus display technology. BacMam virus-based surface display strategies could serve as effective tools in designing vaccines against IB and other infectious diseases. Copyright © 2013. Published by Elsevier Ltd.

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters.

PubMed

Othoum, Ghofran; Bougouffa, Salim; Razali, Rozaimi; Bokhari, Ameerah; Alamoudi, Soha; Antunes, André; Gao, Xin; Hoehndorf, Robert; Arold, Stefan T; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B; Lafi, Feras F; Essack, Magbubah

2018-05-22

The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions. We report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species. B. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.

In vitro effects of preservative-free and preserved prostaglandin analogs on primary cultured human conjunctival fibroblast cells.

PubMed

Kim, Eun Joo; Kim, Yeoun-Hee; Kang, Sun-Hee; Lee, Kyoo Won; Park, Young Jeung

2013-12-01

Long-term use of topical medication is needed for glaucoma treatment. One of the most commonly prescribed classes of hypotensive agents are prostaglandin analogs (PGs) used as both first-line monotherapy; as well as in combination therapy with other hypotensive agents. Several side effects of eye drops can be caused by preservatives. The purpose of this study was to evaluate the effects of PGs with varying concentrations of benzalkonium chloride (BAC), alternative preservatives, or no preservatives on human conjunctival fibroblast cells. Primary human conjunctival fibroblast cells were used in these experiments. Cells were exposed to the following drugs: BAC at different concentrations, bimatoprost 0.01% (with BAC 0.02%), latanoprost 0.005% (with BAC 0.02%), tafluprost 0.0015% with/without 0.001% BAC and travoprost 0.004% (with 0.001% Polyquad) for 15 and 30 minutes. Cell cytotoxicity was evaluated by phase-contrast microscopy to monitor morphological changes of cells, Counting Kit-8 (CCK-8) assay to cell viability, and fluorescent activated cell sorting (FACS) analysis to measure apoptosis. BAC caused cell shrinkage and detachment from the plate in a dose-dependent manner. Morphological changes were observed in cells treated with bimatoprost 0.01% and latanoprost 0.005%. However, mild cell shrinkage was noted in cells treated with tafluprost 0.0015%, while a non-toxic effect was noted with travoprost 0.004% and preservative-free tafluprost 0.0015%. CCK-8 assay and FACS analysis showed all groups had a significantly decreased cell viability and higher apoptosis rate compared with the control group. However, travoprost 0.004% and preservative-free tafluprost 0.0015% showed lower cytotoxicity and apoptosis rate than other drugs. This in vitro study revealed that BAC-induced cytotoxicity is dose-dependent, although it is important to emphasize that the clinical significance of toxicity differences observed among the different PGs formulations has not yet been firmly established. Alternatively preserved or preservative-free glaucoma medications seem to be a reasonable and viable alternative to those preserved with BAC.

In Vitro Effects of Preservative-free and Preserved Prostaglandin Analogs on Primary Cultured Human Conjunctival Fibroblast Cells

PubMed Central

Kim, Eun Joo; Kim, Yeoun-Hee; Kang, Sun-Hee; Lee, Kyoo Won

2013-01-01

Purpose Long-term use of topical medication is needed for glaucoma treatment. One of the most commonly prescribed classes of hypotensive agents are prostaglandin analogs (PGs) used as both first-line monotherapy; as well as in combination therapy with other hypotensive agents. Several side effects of eye drops can be caused by preservatives. The purpose of this study was to evaluate the effects of PGs with varying concentrations of benzalkonium chloride (BAC), alternative preservatives, or no preservatives on human conjunctival fibroblast cells. Methods Primary human conjunctival fibroblast cells were used in these experiments. Cells were exposed to the following drugs: BAC at different concentrations, bimatoprost 0.01% (with BAC 0.02%), latanoprost 0.005% (with BAC 0.02%), tafluprost 0.0015% with/without 0.001% BAC and travoprost 0.004% (with 0.001% Polyquad) for 15 and 30 minutes. Cell cytotoxicity was evaluated by phase-contrast microscopy to monitor morphological changes of cells, Counting Kit-8 (CCK-8) assay to cell viability, and fluorescent activated cell sorting (FACS) analysis to measure apoptosis. Results BAC caused cell shrinkage and detachment from the plate in a dose-dependent manner. Morphological changes were observed in cells treated with bimatoprost 0.01% and latanoprost 0.005%. However, mild cell shrinkage was noted in cells treated with tafluprost 0.0015%, while a non-toxic effect was noted with travoprost 0.004% and preservative-free tafluprost 0.0015%. CCK-8 assay and FACS analysis showed all groups had a significantly decreased cell viability and higher apoptosis rate compared with the control group. However, travoprost 0.004% and preservative-free tafluprost 0.0015% showed lower cytotoxicity and apoptosis rate than other drugs. Conclusions This in vitro study revealed that BAC-induced cytotoxicity is dose-dependent, although it is important to emphasize that the clinical significance of toxicity differences observed among the different PGs formulations has not yet been firmly established. Alternatively preserved or preservative-free glaucoma medications seem to be a reasonable and viable alternative to those preserved with BAC. PMID:24311931

Genetic analysis of the Rhizobium meliloti bacA gene: functional interchangeability with the Escherichia coli sbmA gene and phenotypes of mutants.

PubMed Central

Ichige, A; Walker, G C

1997-01-01

The Rhizobium meliloti bacA gene encodes a function that is essential for bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homolog of BacA, SbmA, is implicated in the uptake of microcin B17, microcin J25 (formerly microcin 25), and bleomycin. When expressed in E. coli with the lacZ promoter, the R. meliloti bacA gene was found to suppress all the known defects of E. coli sbmA mutants, namely, increased resistance to microcin B17, microcin J25, and bleomycin, demonstrating the functional similarity between the two proteins. The R. meliloti bacA386::Tn(pho)A mutant, as well as a newly constructed bacA deletion mutant, was found to show increased resistance to bleomycin. However, it also showed increased resistance to certain aminoglycosides and increased sensitivity to ethanol and detergents, suggesting that the loss of bacA function causes some defect in membrane integrity. The E. coli sbmA gene suppressed all these bacA mutant phenotypes as well as the Fix- phenotype when placed under control of the bacA promoter. Taken together, these results strongly suggest that the BacA and SbmA proteins are functionally similar and thus provide support for our previous hypothesis that BacA may be required for uptake of some compound that plays an important role in bacteroid development. However, the additional phenotypes of bacA mutants identified in this study suggest the alternative possibility that BacA may be needed for membrane integrity, which is likely to be critically important during the early stages of bacterial differentiation within plant cells. PMID:8982000

Drinking and driving in the United States: comparing results from the 2007 and 1996 National Roadside Surveys.

PubMed

Kelley-Baker, Tara; Lacey, John H; Voas, Robert B; Romano, Eduardo; Yao, Jie; Berning, Amy

2013-01-01

The objectives of this study were to (a) use data from the 2007 National Roadside Survey (NRS) to determine the characteristics of weekend nighttime drivers with positive blood alcohol concentrations (BACs) on U.S. roads in 2007; (b) determine the relationship of the driving environment and trip characteristics associated with drinking drivers; and (c) compare the findings for the 2007 NRS with those for the 1996 NRS. Like the 1996 NRS, the 2007 NRS used a stratified random national roadside survey sample of the contiguous 48 states and collected nighttime data on Fridays and Saturdays between 10 p.m. and 3 a.m. Officers directed 8384 drivers into off-road parking areas where our research team asked them to participate in the survey. Of those approached, 7159 (85.4%) provided a breath test. Results revealed that 12 percent of the nighttime drivers had positive BACs, and of those, 2 percent were higher than the 0.08 BAC illegal limit in the United States. Since the 1996 NRS, we found significant reductions in the percentage of BAC-positive drivers across different demographic groups. Age was among the most significant factors associated with a weekend driver having a positive BAC. The probability that a driver would be drinking peaked in the 21- to 25-year-old age group. Male drivers were more likely than female drivers to be drinking, and Asian and Hispanic drivers were less likely than white drivers to be drinking. Drinking drivers were more likely to be driving short distances (5 or fewer miles) late at night (between 1 and 3 a.m.) and to be coming from a bar or restaurant. Finally, 26 percent of the drivers who reported that they would drive less than 5 miles on the night of the survey had positive BACs, compared to only 16 percent who indicated that they would drive between 6 and 20 miles and 10 percent who planned to drive more than 20 miles. The 2007 NRS provides another benchmark in the 4-decade record of drinking drivers on American roads and provides a basis for measuring progress in combating driving under the influence during the coming decade.

Beneficial rhizobacteria from rice rhizosphere confers high protection against biotic and abiotic stress inducing systemic resistance in rice seedlings.

PubMed

Lucas, Jose Antonio; García-Cristobal, Jorge; Bonilla, Alfonso; Ramos, Beatriz; Gutierrez-Mañero, Javier

2014-09-01

The present study reports a screening for PGPR in a highly selective environment, the rhizosphere of rice plants, in southwestern of Spain. Among the 900 isolates, only 38% were positive for at least one of the biochemical activities to detect putative PGPR. The best 80 isolates were selected and identified by 16S rRNA partial sequencing. Among these, 13 strains were selected for growth promotion assays. Only one strain (BaC1-38) was able to significantly increase height, while nine strains significantly inhibited it. Five strains significantly increased dry weight, and only BaC1-21 significantly decreased it. Based on significant modifications in growth, three bacteria (BaC1-13, BaC1-21 and BaC1-38) were tested for systemic induction of resistance against stress challenge (salt and Xanthomonas campestris infection). Protection against salt stress and pathogen infection was similar; BaC1-38 protected by 80%, BaC1-13 by 50% and BaC1-21 only by 20%. Toxicity of salt stress to the plants was evaluated by photosynthetic efficiency of seedlings. Fv/Fm only decreased significantly in plants inoculated with BaC1-13. ΦPSII also decreased significantly in plants inoculated with BaC1-21, but increased significantly with BaC1-38. NPQ decreased significantly in plants inoculated with BaC1-21. The two strains able to induce systemic resistance against Xanthomonas campestris seem to work by different pathways. BaC1-13 primed enzymes related with the detoxification of reactive oxygen species (ROS). However, BaC1-38 primed pathogenesis-related proteins (PRs), and this pathway was more effective, both improved chlorophyll index confirming the priming state of the plant. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

PubMed Central

2012-01-01

Background The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes. PMID:22672252

Sorption and leaching of benzalkonium chlorides in agricultural soils.

PubMed

Khan, Adnan Hossain; Macfie, Sheila M; Ray, Madhumita B

2017-07-01

The adsorption and leaching characteristics of two commonly used benzalkonium chlorides (BACs), benzyl dimethyl dodecyl ammonium chloride (BDDA) and benzyl dimethyl tetradecyl ammonium chloride (BDTA) using three agricultural soils with varied proportions of silt, sand, clay, and organic matter were determined. BACs are cationic surfactants used in large quantities for sanitary and personal care products and are abundant in environmental samples. Adsorption isotherm data (aqueous concentration in the range of 25-150 mg L -1 ) fitted the Langmuir model better than the Freundlich model. BDTA with a longer alkyl chain adsorbed more to soil compared to BDDA, and the soil with the highest percentage of clay adsorbed the most. Column tests conducted using soils amended with lime stabilised biosolids and artificial rain water at a flow rate of 0.2 mL min -1 indicate very low leaching of BACs. Less than 1% of the available BDDA leached through sandy loam soil column with a depth of 9 cm. Therefore, the possibility of BACs to become bioavailable through leaching is very low at environmentally relevant concentrations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Emotional Intelligence and cognitive abilities - associations and sex differences.

PubMed

Pardeller, Silvia; Frajo-Apor, Beatrice; Kemmler, Georg; Hofer, Alex

2017-09-01

In order to expand on previous research, this cross-sectional study investigated the relationship between Emotional Intelligence (EI) and cognitive abilities in healthy adults with a special focus on potential sex differences. EI was assessed by means of the Mayer-Salovey-Caruso-Emotional-Intelligence Test (MSCEIT), whereas cognitive abilities were investigated using the Brief Assessment of Cognition in Schizophrenia (BACS), which measures key aspects of cognitive functioning, i.e. verbal memory, working memory, motor speed, verbal fluency, attention and processing speed, and reasoning and problem solving. 137 subjects (65% female) with a mean age of 38.7 ± 11.8 years were included into the study. While males and females were comparable with regard to EI, men achieved significantly higher BACS composite scores and outperformed women in the BACS subscales motor speed, attention and processing speed, and reasoning and problem solving. Verbal fluency significantly predicted EI, whereas the MSCEIT subscale understanding emotions significantly predicted the BACS composite score. Our findings support previous research and emphasize the relevance of considering cognitive abilities when assessing ability EI in healthy individuals.

Assessment of bacterial endospore viability with fluorescent dyes.

PubMed

Laflamme, C; Lavigne, S; Ho, J; Duchaine, C

2004-01-01

To validate three fluorescence viability assays designed primarily for vegetative cells on pure Bacillus endospores. Purified fresh and gamma-irradiated Bacillus endospores (Bacillus cereus, B. coagulans and two strains of B. subtilis) were used. The viability assays were: 5-cyano-2,3-diotolyl tetrazolium chloride (CTC) to test respiratory activity and early germination, DiBAC4(3) and Live/Dead BacLight to measure membrane energization and permeabilization, respectively. Gamma irradiation treatment completely eliminated spore culturability and was used as negative control. The untreated spores showed respiratory activity after 1 h of incubation and this was characteristic of almost 100% of spores after 24 h. The membrane potential assessment gave no answer about spore viability. A lower proportion of untreated spores had permeabilized membrane compared with gamma-irradiated spores using Live/Dead BacLight (P < 0.02). It is possible to use CTC and Live/Dead BacLight to rapidly test endospore viability and evaluate the proportion of spores in a preparation that could not be recovered with plate count. This study shows that fluorescence tests could be applied to assess viability in potentially pathogenic Bacillus spore preparations within 1 h.

Biomethanation of Sewage Sludge with Food Waste Leachate Via Co-Digestion.

PubMed

Shin, Jingyeong; Kim, Young Beom; Jeon, Jong Hun; Choi, Sangki; Park, In Kyu; Kim, Young Mo

2017-08-28

Anaerobic mono- and co-digestion of sewage sludge and food waste leachate (FWL) were performed by assessing methane production and characterizing microbial communities. Anaerobic digestion (AD) of waste activated sludge (WAS) alone produced the lowest methane (281 ml CH 4 ), but an approximately 80% increase in methane production was achieved via co-digestion of WAS and FWL (506 ml CH 4 ). There were less differences in the diversity of bacterial communities in anaerobic digesters, while archaeal (ARC) and bacterial (BAC) amounts reflected AD performance. Compared with the total ARC and BAC amounts in the mono-digestion of WAS, the ARC and BAC amounts increased two and three times, respectively, during co-digestion of FWL and WAS. In characterized archaeal communities, the dominant ratio of hydrogenotrophic methanogens in the mono-digestion of WAS approached nearly a 1:1 ratio of the two acetoclastic and hydrogenotrophic methanogens in the co-digestion of FWL and WAS. The ARC/BAC ratio in the digesters varied in the range of 5.9% to 9.1%, indicating a positive correlation with the methane production of AD.

ALA-Butyrate prodrugs for Photo-Dynamic Therapy

NASA Astrophysics Data System (ADS)

Berkovitch, G.; Nudelman, A.; Ehenberg, B.; Rephaeli, A.; Malik, Z.

2010-05-01

The use of 5-aminolevulinic acid (ALA) administration has led to many applications of photodynamic therapy (PDT) in cancer. However, the hydrophilic nature of ALA limits its ability to penetrate the cells and tissues, and therefore the need for ALA derivatives became an urgent research target. In this study we investigated the activity of novel multifunctional acyloxyalkyl ester prodrugs of ALA that upon metabolic hydrolysis release active components such as, formaldehyde, and the histone deacetylase inhibitory moiety, butyric acid. Evaluation of these prodrugs under photo-irradiation conditions showed that butyryloxyethyl 5-amino-4-oxopentanoate (ALA-BAC) generated the most efficient photodynamic destruction compared to ALA. ALA-BAC stimulated a rapid biosynthesis of protoporphyrin IX (PpIX) in human glioblastoma U-251 cells which resulted in generation of intracellular ROS, reduction of mitochondrial activity, leading to apoptotic and necrotic death of the cells. The apoptotic cell death induced by ALA / ALA-BAC followed by PDT equally activate intrinsic and extrinsic apoptotic signals and both pathways may occur simultaneously. The main advantage of ALA-BAC over ALA stems from its ability to induce photo-damage at a significantly lower dose than ALA.

'Wide-awake drunkenness'? Investigating the association between alcohol intoxication and stimulant use in the night-time economy.

PubMed

Pennay, Amy; Miller, Peter; Busija, Lucy; Jenkinson, Rebecca; Droste, Nicolas; Quinn, Brendan; Jones, Sandra C; Lubman, Dan I

2015-02-01

We tested whether patrons of the night-time economy who had co-consumed energy drinks or illicit stimulants with alcohol had higher blood alcohol concentration (BAC) levels than patrons who had consumed only alcohol. Street intercept surveys (n = 4227) were undertaken between 9 p.m. and 5 a.m. over a period of 7 months. Interviews were undertaken with patrons walking through entertainment precincts, queuing to enter venues or exiting venues in five Australian cities. The response rate was 92.1%; more than half the study sample was male (60.2%) and the median age was 23 years (range 18-72). Data were collected on demographics, length of drinking session, venue types visited, types and quantity of alcohol consumed and other substance use. A BAC reading was recorded and a subsample of participants was tested for other drug use. Compared with the total sample (0.068%), illicit stimulant consumers (0.080%; P = 0.004) and energy drink consumers (0.074%; P < 0.001) had a significantly higher median BAC reading, and were more likely to engage in pre-drinking (65.6, 82.1 and 77.6%, respectively, P < 0.001) and longer drinking sessions (4, 5 and 4.5 hours, respectively, P < 0.001). However, stimulant use was not associated independently with higher BAC in the final multivariable model (illicit stimulants P = 0.198; energy drinks P = 0.112). Interaction analyses showed that stimulant users had a higher BAC in the initial stages of the drinking session, but not after 4-6 hours. While stimulant use does not predict BAC in and of itself, stimulants users are more likely to engage in prolonged sessions of heavy alcohol consumption and a range of risk-taking behaviours on a night out, which may explain higher levels of BAC among stimulants users, at least in the initial stages of the drinking session. © 2014 Society for the Study of Addiction.

Sex-Linked Pheromone Receptor Genes of the European Corn Borer, Ostrinia nubilalis, Are in Tandem Arrays

PubMed Central

Yasukochi, Yuji; Miura, Nami; Nakano, Ryo; Sahara, Ken; Ishikawa, Yukio

2011-01-01

Background Tuning of the olfactory system of male moths to conspecific female sex pheromones is crucial for correct species recognition; however, little is known about the genetic changes that drive speciation in this system. Moths of the genus Ostrinia are good models to elucidate this question, since significant differences in pheromone blends are observed within and among species. Odorant receptors (ORs) play a critical role in recognition of female sex pheromones; eight types of OR genes expressed in male antennae were previously reported in Ostrinia moths. Methodology/Principal Findings We screened an O. nubilalis bacterial artificial chromosome (BAC) library by PCR, and constructed three contigs from isolated clones containing the reported OR genes. Fluorescence in situ hybridization (FISH) analysis using these clones as probes demonstrated that the largest contig, which contained eight OR genes, was located on the Z chromosome; two others harboring two and one OR genes were found on two autosomes. Sequence determination of BAC clones revealed the Z-linked OR genes were closely related and tandemly arrayed; moreover, four of them shared 181-bp direct repeats spanning exon 7 and intron 7. Conclusions/Significance This is the first report of tandemly arrayed sex pheromone receptor genes in Lepidoptera. The localization of an OR gene cluster on the Z chromosome agrees with previous findings for a Z-linked locus responsible for O. nubilalis male behavioral response to sex pheromone. The 181-bp direct repeats might enhance gene duplications by unequal crossovers. An autosomal locus responsible for male response to sex pheromone in Heliothis virescens and H. subflexa was recently reported to contain at least four OR genes. Taken together, these findings support the hypothesis that generation of additional copies of OR genes can increase the potential for male moths to acquire altered specificity for pheromone components, and accordingly, facilitate differentiation of sex pheromones. PMID:21526121

Radiation exposure, and procedure and fluoroscopy times in endovascular treatment of intracranial aneurysms: a methodological comparison.

PubMed

Cheung, Nicholas K; Boutchard, Michelle; Carr, Michael W; Froelich, Jens J

2018-01-09

Limited data are available for radiation exposure, and procedure and fluoroscopy times in neuroendovascular treatment (NET) strategies. This study establishes and compares related parameters between coil embolization (COIL), balloon assisted coil embolization (BAC), stent assisted coil embolization (SAC), and flow diverting technology (FDT) in NET of intracranial aneurysms. Between 2010 and 2017, 249 consecutive intracranial aneurysms underwent NET at a single center, all performed by the same operator. Dose area products (DAP), and procedure and fluoroscopy times were recorded and compared between COIL, BAC, SAC, and FDT techniques. Differences in parameters between cohorts were analyzed for significance using the Mann-Whitney U test, unpaired t test and χ 2 test. Additional subgroup analysis was performed for emergency and elective cases. 83 aneurysms were treated with COIL (33%), 72 with BAC (29%), 61 with SAC (25%), and 33 with FDT (13%). Baseline characteristics were largely similar within these groups (P>0.05). Among COIL, BAC, and FDT cohorts, no significant difference was found for mean DAP, or procedure and fluoroscopy times (P>0.05). However, compared with all other cohorts, SAC was associated with a significantly higher DAP and longer procedure and fluoroscopy times (P<0.005). No significant difference was recorded for emergency and elective case subgroups. Compared with other NET strategies, SAC was associated with a significantly higher DAP, and longer procedure and fluoroscopy times. This study provides an initial dataset regarding radiation exposure, and procedure and fluoroscopy times for common NET, and may assist ALARA (As Low As Reasonably Achievable) principles to reduce radiation risks. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

An Efficient Method for High-Fidelity BAC/PAC Retrofitting with a Selectable Marker for Mammalian Cell Transfection

PubMed Central

Wang, Zunde; Engler, Peter; Longacre, Angelika; Storb, Ursula

2001-01-01

Large-scale genomic sequencing projects have provided DNA sequence information for many genes, but the biological functions for most of them will only be known through functional studies. Bacterial artificial chromosomes (BACs) and P1-derived artificial chromosomes (PACs) are large genomic clones stably maintained in bacteria and are very important in functional studies through transfection because of their large size and stability. Because most BAC or PAC vectors do not have a mammalian selection marker, transfecting mammalian cells with genes cloned in BACs or PACs requires the insertion into the BAC/PAC of a mammalian selectable marker. However, currently available procedures are not satisfactory in efficiency and fidelity. We describe a very simple and efficient procedure that allows one to retrofit dozens of BACs in a day with no detectable deletions or unwanted recombination. We use a BAC/PAC retrofitting vector that, on transformation into competent BAC or PAC strains, will catalyze the specific insertion of itself into BAC/PAC vectors through in vivo cre/loxP site-specific recombination. PMID:11156622

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

PubMed Central

Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Stoffel, Kevin; Zheng, Xiuting; Saski, Christopher A.; Scheffler, Brian E.; Fang, David D.; Chen, Z. Jeffrey; Van Deynze, Allen; Stelly, David M.

2015-01-01

A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies. PMID:25858960

The effects of moderate alcohol concentrations on driving and cognitive performance during ascending and descending blood alcohol concentrations.

PubMed

Starkey, Nicola J; Charlton, Samuel G

2014-07-01

Alcohol has an adverse effect on driving performance; however, the effects of moderate doses on different aspects of the driving task are inconsistent and differ across the intoxication curve. This research aimed to investigate driving and cognitive performance asymmetries (acute tolerance and acute protracted error) accompanying the onset and recovery from moderate alcohol consumption. Sixty-one participants received a placebo, medium (target blood alcohol concentration [BAC] 0.05 mg/ml) or high (target BAC 0.08 mg/ml) dose of alcohol. Participants completed a simulated drive, cognitive tests and subjective rating scales five times over a 3.5 h period. When ascending and descending BACs (0.05 and 0.09 mg/ml) were compared participants' self-ratings of intoxication and willingness to drive showed acute tolerance. Acute protracted errors were observed for response speed, maze learning errors, time exceeding the speed limit and exaggerated steering responses to hazards. Participants' estimates of their level of intoxication were poorly related to their actual BAC levels (and hence degree of impairment), and various aspects of driving and cognitive performance worsened during descending BACs. This indicates that drivers are not good at judging their fitness to drive after drinking only moderate amounts of alcohol and suggests an important focus for public education regarding alcohol and driving. Copyright © 2014 John Wiley & Sons, Ltd.

Generation of a Gaussia luciferase-expressing endotheliotropic cytomegalovirus for screening approaches and mutant analyses.

PubMed

Falk, Jessica J; Laib Sampaio, Kerstin; Stegmann, Cora; Lieber, Diana; Kropff, Barbara; Mach, Michael; Sinzger, Christian

2016-09-01

For many questions in human cytomegalovirus (HCMV) research, assays are desired that allow robust and fast quantification of infection efficiencies under high-throughput conditions. The secreted Gaussia luciferase has been demonstrated as a suitable reporter in the context of a fibroblast-adapted HCMV strain, which however is greatly restricted in the number of cell types to which it can be applied. We inserted the Gaussia luciferase expression cassette into the BAC-cloned virus strain TB40-BAC4, which displays the natural broad cell tropism of HCMV and hence allows application to screening approaches in a variety of cell types including fibroblasts, epithelial, and endothelial cells. Here, we applied the reporter virus TB40-BAC4-IE-GLuc to identify mouse hybridoma clones that preferentially neutralize infection of endothelial cells. In addition, as the Gaussia luciferase is secreted into culture supernatants from infected cells it allows kinetic analyses in living cultures. This can speed up and facilitate phenotypic characterization of BAC-cloned mutants. For example, we analyzed a UL74 stop-mutant of TB40-BAC4-IE-GLuc immediately after reconstitution in transfected cultures and found the increase of luciferase delayed and reduced as compared to wild type. Phenotypic monitoring directly in transfected cultures can minimize the risk of compensating mutations that might occur with extended passaging. Copyright © 2016 Elsevier B.V. All rights reserved.

Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization.

PubMed

Jiang, Likun; You, Weiwei; Zhang, Xiaojun; Xu, Jian; Jiang, Yanliang; Wang, Kai; Zhao, Zixia; Chen, Baohua; Zhao, Yunfeng; Mahboob, Shahid; Al-Ghanim, Khalid A; Ke, Caihuan; Xu, Peng

2016-02-01

The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.

Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird

PubMed Central

2009-01-01

Background With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. Results From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. Conclusion Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species. PMID:19607659

Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird.

PubMed

Chapus, Charles; Edwards, Scott V

2009-07-14

With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.

Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy

PubMed Central

2011-01-01

Background DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery. Results We have observed that (1) the Tol2 transposase (but not piggyBac) is highly sensitive to molecular engineering; (2) the piggyBac donor with only the 40 bp 3'-and 67 bp 5'-terminal repeat domain is sufficient for effective transposition; and (3) a small amount of piggyBac transposases results in robust transposition suggesting the piggyBac transpospase is highly active. Performing genome-wide target profiling on data sets obtained by retrieving chromosomal targeting sequences from individual clones, we have identified several piggyBac and Tol2 hotspots and observed that (4) piggyBac and Tol2 display a clear difference in targeting preferences in the human genome. Finally, we have observed that (5) only sites with a particular sequence context can be targeted by either piggyBac or Tol2. Conclusions The non-overlapping targeting preference of piggyBac and Tol2 makes them complementary research tools for manipulating mammalian genomes. PiggyBac is the most promising transposon-based vector system for achieving site-specific targeting of therapeutic genes due to the flexibility of its transposase for being molecularly engineered. Insights from this study will provide a basis for engineering piggyBac transposases to achieve site-specific therapeutic gene targeting. PMID:21447194

Perception of intoxication in a field study of the night-time economy: Blood alcohol concentration, patron characteristics, and event-level predictors.

PubMed

Kaestle, Christine E; Droste, Nicolas; Peacock, Amy; Bruno, Raimondo; Miller, Peter

2018-01-01

Determine the relationship of subjective intoxication to blood alcohol concentration (BAC) and examine whether patron and event-level characteristics modify the relationship of BAC to subjective intoxication. An in-situ systematic random sample of alcohol consumers attending night-time entertainment districts between 10pm and 3am on Friday and Saturday nights in five Australian cities completed a brief interview (n=4628). Participants reported age, sex, and pre-drinking, energy drink, tobacco, illicit stimulant and other illicit drug use that night, and their subjective intoxication and BAC were assessed. Male and female drinkers displayed equally low sensitivity to the impact of alcohol consumption when self-assessing their intoxication (BAC only explained 19% of variance). The marginal effect of BAC was not constant. At low BAC, participants were somewhat sensitive to increases in alcohol consumption, but at higher BAC levels that modest sensitivity dissipated (actual BAC had less impact on self-assessed intoxication). The slope ultimately leveled out to be non-responsive to additional alcohol intake. Staying out late, pre-drinking, and being young introduced biases resulting in higher self-assessed intoxication regardless of actual BAC. Further, both energy drinks and stimulant use modified the association between BAC and perceived intoxication, resulting in more compressed changes in self-assessment as BAC varies up or down, indicating less ability to perceive differences in BAC level. The ability of intoxicated patrons to detect further intoxication is impaired. Co-consumption of energy drinks and/or stimulant drugs is associated with impaired intoxication judgment, creating an additional challenge for the responsible service and consumption of alcohol. Copyright © 2017 Elsevier Ltd. All rights reserved.

Heterologous Complementation Reveals a Specialized Activity for BacA in the Medicago-Sinorhizobium meliloti Symbiosis.

PubMed

diCenzo, George C; Zamani, Maryam; Ludwig, Hannah N; Finan, Turlough M

2017-04-01

The bacterium Sinorhizobium meliloti Rm2011 forms N 2 -fixing root nodules on alfalfa and other leguminous plants. The pSymB chromid contains a 110-kb region (the ETR region) showing high synteny to a chromosomally located region in Sinorhizobium fredii NGR234 and related rhizobia. We recently introduced the ETR region from S. fredii NGR234 into the S. meliloti chromosome. Here, we report that, unexpectedly, the S. fredii NGR234 ETR region did not complement deletion of the S. meliloti ETR region in symbiosis with Medicago sativa. This phenotype was due to the bacA gene of NGR234 not being functionally interchangeable with the S. meliloti bacA gene during M. sativa symbiosis. Further analysis revealed that, whereas bacA genes from S. fredii or Rhizobium leguminosarum bv. viciae 3841 failed to complement the Fix - phenotype of a S. meliloti bacA mutant with M. sativa, they allowed for further developmental progression prior to a loss of viability. In contrast, with Melilotus alba, bacA from S. fredii and R. leguminosarum supported N 2 fixation by a S. meliloti bacA mutant. Additionally, the S. meliloti bacA gene can support N 2 fixation of a R. leguminosarum bacA mutant during symbiosis with Pisum sativum. A phylogeny of BacA proteins illustrated that S. meliloti BacA has rapidly diverged from most rhizobia and has converged toward the sequence of pathogenic genera Brucella and Escherichia. These data suggest that the S. meliloti BacA has evolved toward a specific interaction with Medicago and highlights the limitations of using a single model system for the study of complex biological topics.

Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies

PubMed Central

2012-01-01

Background Array comparative genomic hybridization (CGH) has been repeatedly shown to be a successful tool for the identification of genomic variations in a clinical population. During the last decade, the implementation of array CGH has resulted in the identification of new causative submicroscopic chromosome imbalances and copy number variations (CNVs) in neuropsychiatric (neurobehavioral) diseases. Currently, array-CGH-based technologies have become an integral part of molecular diagnosis and research in individuals with neuropsychiatric disorders and children with intellectual disability (mental retardation) and congenital anomalies. Here, we introduce the Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies analyzed by BAC array CGH and a novel bioinformatic strategy. Results Among 54 individuals highly selected according to clinical criteria and molecular and cytogenetic data (from 2426 patients evaluated cytogenetically and molecularly between November 2007 and May 2012), chromosomal imbalances were detected in 26 individuals (48%). In two patients (4%), a previously undescribed condition was observed. The latter has been designated as meiotic (constitutional) genomic instability resulted in multiple submicroscopic rearrangements (including CNVs). Using bioinformatic strategy, we were able to identify clinically relevant CNVs in 15 individuals (28%). Selected cases were confirmed by molecular cytogenetic and molecular genetic methods. Eight out of 26 chromosomal imbalances (31%) have not been previously reported. Among them, three cases were co-occurrence of subtle chromosome 9 and 21 deletions. Conclusions We conducted an array CGH study of Russian patients suffering from intellectual disability, autism, epilepsy and congenital anomalies. In total, phenotypic manifestations of clinically relevant genomic variations were found to result from genomic rearrangements affecting 1247 disease-causing and pathway-involved genes. Obviously, a significantly lesser part of them are true candidates for intellectual disability, autism or epilepsy. The success of our preliminary array CGH and bioinformatic study allows us to expand the cohort. According to the available literature, this is the first comprehensive array CGH evaluation of a Russian cohort of children with neuropsychiatric disorders and congenital anomalies. PMID:23272938

The leaves of Diospyros kaki exert beneficial effects on a benzalkonium chloride-induced murine dry eye model.

PubMed

Kim, Kyung-A; Hyun, Lee Chung; Jung, Sang Hoon; Yang, Sung Jae

2016-01-01

In this study, the beneficial effects of the oral administration of ethanol extract of Diospyros kaki (EEDK) were tested on a mouse dry eye model induced by benzalkonium chloride (BAC). A solution of 0.2% BAC was administered topically to mouse eyes for 14 days, twice daily, to induce dry eye. Various concentrations of EEDK were administrated daily by oral gavage for 14 days after BAC treatment. Preservative-free eye drops were instilled in the positive-control group. The tear secretion volume (Schirmer's test), tear break-up time (BUT), and fluorescein score were measured on the ocular surface. BAC-induced corneal damage was tested with hematoxylin-eosin staining. Moreover, apoptotic cell death in the corneal epithelial layer was investigated with terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) staining. The protein expression level of interleukin-1alpha (IL-1α), IL-1β, IL-6, tumor necrosis factor- alpha (TNF-α), and monocyte chemotactic protein-1 (MCP-1) was determined with western blot analysis. Furthermore, squamous metaplasia in the corneal epithelial layer was detected with immunofluorescent staining for cytokeratine-10. The cellular proliferation in the cornea was examined with immunohistochemical staining for Ki-67. EEDK treatment resulted in prolonged BUT, decreased fluorescein score, increased tear volume, and smoother epithelial cells compared with BAC treatment alone in the cornea. Moreover, EEDK treatment inhibited the inflammatory response and corneal epithelial cell death in a BAC-induced murine dry eye model, and changes in squamous cells were inhibited. Proliferative activity in the corneal epithelium cells was improved with EEDK. EEDK could be a potential therapeutic agent in the clinical treatment of dry eye.

The association of alcohol consumption with patient survival after organophosphate poisoning: a multicenter retrospective study.

PubMed

Lee, Young Hwan; Oh, Young Taeck; Lee, Won Woong; Ahn, Hee Cheol; Sohn, You Dong; Ahn, Ji Yun; Min, Yong Hun; Kim, Hyun; Lim, Seung Wook; Lee, Kui Ja; Shin, Dong Hyuk; Park, Sang O; Park, Seung Min

2017-06-01

Organophosphate (OP) intoxication remains a serious worldwide health concern, and many patients with acute OP intoxication have also consumed alcohol. Therefore, we evaluated the association of blood alcohol concentration (BAC) with mortality among patients with OP intoxication. We retrospectively reviewed records from 135 patients who were admitted to an emergency department (ED) for OP intoxication between January 2000 and December 2012. Factors that were associated with patient survival were identified via receiver operating characteristic curve, multiple logistic regression, and Kaplan-Meier survival analyses. Among 135 patients with acute OP poisoning, 112 patients survived (overall mortality rate: 17 %). The non-survivors also exhibited a significantly higher BAC, compared to the survivors [non-survivors: 192 mg/dL, interquartile range (IQR) 97-263 mg/dL vs. survivors: 80 mg/dL, IQR 0-166.75 mg/dL; p < 0.001]. A BAC cut-off value of 173 mg/dL provided an area under the curve of 0.744 [95 % confidence interval (CI) 0.661-0.815], a sensitivity of 65.2 %, and a specificity of 81.2 %. A BAC of >173 mg/dL was associated with a significantly increased risk of 6-month mortality in the multiple logistic regression model (odds ratio 4.92, 95 % CI 1.45-16.67, p = 0.001). The Cox proportional hazard model revealed that a BAC of >173 mg/dL provided a hazard ratio of 3.07 (95 % CI 1.19-7.96, p = 0.021). A BAC of >173 mg/dL is a risk factor for mortality among patients with OP intoxication.

Quantifying the combined effects of pronase and benzalkonium chloride in removing late-stage Listeria monocytogenes-Escherichia coli dual-species biofilms.

PubMed

Rodríguez-López, Pedro; Puga, Carmen H; Orgaz, Belén; Cabo, Marta L

2017-09-01

This work presents the assessment of the effectivity of a pronase (PRN)-benzalkonium chloride (BAC) sequential treatment in removing Listeria monocytogenes-Escherichia coli dual-species biofilms grown on stainless steel (SS) using fluorescence microscopy and plate count assays. The effects of PRN-BAC on the occupied area (OA) by undamaged cells in 168 h dual-species samples were determined using a first-order factorial design. Empirical equations significantly (r 2 = 0.927) described a negative individual effect of BAC and a negative interactive effect of PRN-BAC achieving OA reductions up to 46%. After treatment, high numbers of remaining attached and released viable and cultivable E. coli cells were detected in PRN-BAC combinations when low BAC concentrations were used. Therefore, at appropriate BAC doses, in addition to biofilm removal, sequential application of PRN and BAC represents an appealing strategy for pathogen control on SS surfaces while hindering the dispersion of live cells into the environment.

Effect of temperature and benzalkonium chloride on nitrate reduction.

PubMed

Hajaya, Malek G; Tezel, Ulas; Pavlostathis, Spyros G

2011-04-01

The effect of temperature and benzalkonium chloride (BAC) on nitrate reduction was investigated in batch assays using a mixed nitrate reducing culture. Nitrate was transformed completely, mainly through denitrification, to dinitrogen at 5, 10, 15 and 22 °C. In the absence of BAC, reduction of individual nitrogen oxides had different susceptibility to temperature and transient nitrite accumulation was observed at low temperatures. When the effect of BAC was tested up to 100 mg/L from 5 to 22 °C, denitrification was inhibited at and above 50mg BAC/L with transient nitrite accumulation at all temperatures. The effect of BAC was described by a competitive inhibition model. Nitrite reduction was the denitrification step most susceptible to BAC, especially at low temperatures. BAC was not degraded during the batch incubation and was mostly biomass-adsorbed. Overall, this study shows that low temperatures exacerbate the BAC inhibitory effect, which in turn is controlled by adsorption to biomass. Copyright © 2011 Elsevier Ltd. All rights reserved.

The relationship of normal body temperature, end-expired breath temperature, and BAC/BrAC ratio in 98 physically fit human test subjects.

PubMed

Cowan, J Mack; Burris, James M; Hughes, James R; Cunningham, Margaret P

2010-06-01

The relationship between normal body temperature, end-expired breath temperature, and blood alcohol concentration (BAC)/breath alcohol concentration (BrAC) ratio was studied in 98 subjects (84 men, 14 women). Subjects consumed alcohol sufficient to produce a BrAC of at least 0.06 g/210 L 45-75 min after drinking. Breath samples were analyzed using an Intoxilyzer 8000 specially equipped to measure breath temperature. Venous blood samples and body temperatures were then taken. The mean body temperature of the men (36.6 degrees C) was lower than the women (37.0 degrees C); however, their mean breath temperatures were virtually identical (men: 34.5 degrees C; women: 34.6 degrees C). The BAC exceeded the BrAC for every subject. BAC/BrAC ratios were calculated from the BAC and BrAC analytical results. There was no difference in the BAC/BrAC ratios for men (1:2379) and women (1:2385). The correlation between BAC and BrAC was high (r = 0.938, p < 0.0001), whereas the correlations between body temperature and end-expired breath temperature, body temperature and BAC/BrAC ratio, and breath temperature and BAC/BrAC ratio were much lower. Neither normal body temperature nor end-expired breath temperature was strongly associated with BAC/BrAC ratio.

An expected utility maximizer walks into a bar…

PubMed

Burghart, Daniel R; Glimcher, Paul W; Lazzaro, Stephanie C

2013-06-01

We conducted field experiments at a bar to test whether blood alcohol concentration (BAC) correlates with violations of the generalized axiom of revealed preference (GARP) and the independence axiom. We found that individuals with BACs well above the legal limit for driving adhere to GARP and independence at rates similar to those who are sober. This finding led to the fielding of a third experiment to explore how risk preferences might vary as a function of BAC. We found gender-specific effects: Men did not exhibit variations in risk preferences across BACs. In contrast, women were more risk averse than men at low BACs but exhibited increasing tolerance towards risks as BAC increased. Based on our estimates, men and women's risk preferences are predicted to be identical at BACs nearly twice the legal limit for driving. We discuss the implications for policy-makers.

Autism-specific copy number variants further implicate the phosphatidylinositol signaling pathway and the glutamatergic synapse in the etiology of the disorder.

PubMed

Cuscó, Ivon; Medrano, Andrés; Gener, Blanca; Vilardell, Mireia; Gallastegui, Fátima; Villa, Olaya; González, Eva; Rodríguez-Santiago, Benjamín; Vilella, Elisabet; Del Campo, Miguel; Pérez-Jurado, Luis A

2009-05-15

Autism spectrum disorders (ASDs) constitute a group of severe neurodevelopmental conditions with complex multifactorial etiology. In order to explore the hypothesis that submicroscopic genomic rearrangements underlie some ASD cases, we have analyzed 96 Spanish patients with idiopathic ASD after extensive clinical and laboratory screening, by array comparative genomic hybridization (aCGH) using a homemade bacterial artificial chromosome (BAC) array. Only 13 of the 238 detected copy number alterations, ranging in size from 89 kb to 2.4 Mb, were present specifically in the autistic population (12 out of 96 individuals, 12.5%). Following validation by additional molecular techniques, we have characterized these novel candidate regions containing 24 different genes including alterations in two previously reported regions of chromosome 7 associated with the ASD phenotype. Some of the genes located in ASD-specific copy number variants act in common pathways, most notably the phosphatidylinositol signaling and the glutamatergic synapse, both known to be affected in several genetic syndromes related with autism and previously associated with ASD. Our work supports the idea that the functional alteration of genes in related neuronal networks is involved in the etiology of the ASD phenotype and confirms a significant diagnostic yield for aCGH, which should probably be included in the diagnostic workup of idiopathic ASD.

Uptake and phytotoxic effect of benzalkonium chlorides in Lepidium sativum and Lactuca sativa.

PubMed

Khan, Adnan Hossain; Libby, Mark; Winnick, Daniel; Palmer, John; Sumarah, Mark; Ray, Madhumita B; Macfie, Sheila M

2018-01-15

Cationic surfactants such as benzalkonium chlorides (BACs) are used extensively as biocides in hospitals, food processing industries, and personal care products. BACs have the potential to reach the rooting zone of crop plants and BACs might thereby enter the food chain. The two most commonly used BACs, benzyl dimethyl dodecyl ammonium chloride (BDDA) and benzyl dimethyl tetradecyl ammonium chloride (BDTA), were tested in a hydroponic system to assess the uptake by and phytotoxicity to lettuce (Lactuca sativa L.) and garden cress (Lepidium sativum L.). Individually and in mixture, BACs at concentrations up to 100 mg L -1 did not affect germination; however, emergent seedlings were sensitive at 1 mg L -1 for lettuce and 5 mg L -1 for garden cress. After 12 d exposure to 0.25 mg L -1 BACs, plant dry weight was reduced by 68% for lettuce and 75% for garden cress, and symptoms of toxicity (necrosis, chlorosis, wilting, etc.) were visible. High performance liquid chromatography-mass spectroscopy analysis showed the presence of BACs in the roots and shoots of both plant species. Although no conclusive relationship was established between the concentrations of six macro- or six micro-nutrients, growth inhibition or BAC uptake, N and Mg concentrations in BAC-treated lettuce were 50% lower than that of control, indicating that BACs might induce nutrient deficiency. Although bioavailability of a compound in hydroponics is significantly higher than that in soil, these results confirm the potential of BACs to harm vascular plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Impact of a Structural Intervention to Address Alcohol Use Among Gay Bar Patrons in San Francisco: The PACE Study.

PubMed

Charlebois, Edwin D; Plenty, Albert H; Lin, Jessica; Ayala, Alicia; Hecht, Jennifer

2017-11-01

We evaluated the impact on alcohol intake and blood alcohol concentration (BAC) of a multi-level structural intervention to increase the availability of free water, coupled with messaging on pacing alcohol intake and normative feedback of blood alcohol concentration in a convenience sample of gay bars in San Francisco. Participants (n = 1,293) were recruited among exiting patrons of four gay bars (two intervention bars and two control bars). Participants were surveyed on alcohol intake and BAC was measured by breathalyzer. Prior to the intervention there were no significant differences in baseline alcohol measures between intervention and control bars. Post-intervention there were significant differences on objective and subjective measures of alcohol consumption: 30% of intervention bar participants had BAC% levels over the legal driving limit (0.08%) compared to 43% of control bar participants, p < 0.0001 and 78% of intervention bar participants were above the AUDIT-C cut-off for hazardous drinking compared to 87% in control bars, p < 0.001.

An expected utility maximizer walks into a bar…

PubMed Central

Glimcher, Paul W.; Lazzaro, Stephanie C.

2013-01-01

We conducted field experiments at a bar to test whether blood alcohol concentration (BAC) correlates with violations of the generalized axiom of revealed preference (GARP) and the independence axiom. We found that individuals with BACs well above the legal limit for driving adhere to GARP and independence at rates similar to those who are sober. This finding led to the fielding of a third experiment to explore how risk preferences might vary as a function of BAC. We found gender-specific effects: Men did not exhibit variations in risk preferences across BACs. In contrast, women were more risk averse than men at low BACs but exhibited increasing tolerance towards risks as BAC increased. Based on our estimates, men and women’s risk preferences are predicted to be identical at BACs nearly twice the legal limit for driving. We discuss the implications for policy-makers. PMID:24244072

Functional characterization of a prokaryotic Kir channel.

PubMed

Enkvetchakul, Decha; Bhattacharyya, Jaya; Jeliazkova, Iana; Groesbeck, Darcy K; Cukras, Catherine A; Nichols, Colin G

2004-11-05

The Kir gene family encodes inward rectifying K+ (Kir) channels that are widespread and critical regulators of excitability in eukaryotic cells. A related gene family (KirBac) has recently been identified in prokaryotes. While a crystal structure of one member, Kir-Bac1.1, has been solved, there has been no functional characterization of any KirBac gene products. Here we present functional characterization of KirBac1.1 reconstituted in liposomes. Utilizing a 86Rb+ uptake assay, we demonstrate that KirBac1.1 generates a K+ -selective permeation path that is inhibited by extraliposomal Ba2+ and Ca2+ ions. In contrast to KcsA (an acid-activated bacterial potassium channel), KirBac1.1 is inhibited by extraliposomal acid (pKa approximately 6). This characterization of KirBac1.1 activity now paves the way for further correlation of structure and function in this model Kir channel.

Breast arterial calcification is associated with reproductive factors in asymptomatic postmenopausal women.

PubMed

Bielak, Lawrence F; Whaley, Dana H; Sheedy, Patrick F; Peyser, Patricia A

2010-09-01

The etiology of breast arterial calcification (BAC) is not well understood. We examined reproductive history and cardiovascular disease (CVD) risk factor associations with the presence of detectable BAC in asymptomatic postmenopausal women. Reproductive history and CVD risk factors were obtained in 240 asymptomatic postmenopausal women from a community-based research study who had a screening mammogram within 2 years of their participation in the study. The mammograms were reviewed for the presence of detectable BAC. Age-adjusted logistic regression models were fit to assess the association between each risk factor and the presence of BAC. Multiple variable logistic regression models were used to identify the most parsimonious model for the presence of BAC. The prevalence of BAC increased with increased age (p < 0.0001). The most parsimonious logistic regression model for BAC presence included age at time of examination, increased parity (p = 0.01), earlier age at first birth (p = 0.002), weight, and an age-by-weight interaction term (p = 0.004). Older women with a smaller body size had a higher probability of having BAC than women of the same age with a larger body size. The presence or absence of BAC at mammography may provide an assessment of a postmenopausal woman's lifetime estrogen exposure and indicate women who could be at risk for hormonally related conditions.

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping.

PubMed

Hulse-Kemp, Amanda M; Ashrafi, Hamid; Stoffel, Kevin; Zheng, Xiuting; Saski, Christopher A; Scheffler, Brian E; Fang, David D; Chen, Z Jeffrey; Van Deynze, Allen; Stelly, David M

2015-04-09

A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies. Copyright © 2015 Hulse-Kemp et al.

Federal actions to incentivise state adoption of 0.08 g/dL blood alcohol concentration laws.

PubMed

Tung, Gregory J; Vernick, Jon S; Stuart, Elizabeth A; Webster, Daniel W; Gielen, Andrea C

2017-10-01

To model rates of 0.08 g/dL blood alcohol concentration (BAC) per se law implementation among the states associated with (1) a federal incentive grant programme and (2) a threat from the federal government to withhold highway transportation funds. An observational study of state-level 0.08 g/dL BAC per se law enactment among all 50 US states from 1982 to 2006 using a parametric survival analysis to assess the time-dependent risk of policy enactment. The federal government's threat to withhold transportation funds was associated with a 10.30 times greater hazard (HR: 10.30, 95% CI 3.88 to 27.36) of states adopting a 0.08 g/dL BAC law compared with periods of time when this threat was not in place. The incentive grant programme created by the federal government was associated with a non-significant 17% decrease in the hazard of states adopting a 0.08 g/dL BAC law (HR: 0.83, 95% CI 0.35 to 2.0). In the case of 0.08 g/dL BAC per se laws, the federal government's threat to withhold transportation funds was effective at accelerating policy adoption. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Facile synthesis of bacitracin-templated palladium nanoparticles with superior electrocatalytic activity

NASA Astrophysics Data System (ADS)

Li, Yanji; Wang, Zi; Li, Xiaoling; Yin, Tian; Bian, Kexin; Gao, Faming; Gao, Dawei

2017-02-01

Palladium nanomaterials have attracted great attention on the development of electrocatalysts for fuel cells. Herein, we depicted a novel strategy in the synthesis of palladium nanoparticles with superior electrocatalytic activity. The new approach, based on the self-assembly of bacitracin biotemplate and palladium salt for the preparation of bacitracin-palladium nanoparticles (Bac-PdNPs), was simple, low-cost, and green. The complex, composed by a series of spherical Bac-PdNPs with a diameter of 70 nm, exhibited a chain-liked morphology in TEM and a face-centered cubic crystal structure in X-Ray diffraction and selected area electron diffraction. The palladium nanoparticles were mono-dispersed and stable in aqueous solution as shown in TEM and zeta potential. Most importantly, compared to the commercial palladium on carbon (Pd/C) catalyst (8.02 m2 g-1), the Bac-PdNPs showed a larger electrochemically active surface area (47.57 m2 g-1), which endowed the products an excellent electrocatalytic activity for ethanol oxidation in alkaline medium. The strategy in synthesis of Bac-PdNPs via biotemplate approach might light up new ideas in anode catalysts for direct ethanol fuel cells.

Comparison of 'time to detection' values between BacT/ALERT VIRTUO and BacT/ALERT 3D instruments for clinical blood culture samples.

PubMed

Congestrì, Francesco; Pedna, Maria Federica; Fantini, Michela; Samuelli, Michela; Schiavone, Pasqua; Torri, Arianna; Bertini, Stefania; Sambri, Vittorio

2017-09-01

The early detection of bacteraemia and fungemia is of paramount importance to guide antimicrobial therapy in septic patients. In this study the 'time to detection' (TTD) value for the new blood culture system BacT/ALERT VIRTUO (VIRTUO) was evaluated in 1462 positive clinical bottles and compared with the TTD for 1601 positive clinical bottles incubated in the BacT/ALERT 3D system (BTA-3D). The most representative microorganisms isolated from bottles incubated in both blood culture systems were divided into eight categories (in order of frequency): coagulase-negative staphylococci (CoNS), Escherichia coli, Enterobacteriaceae (other than E. coli), Staphylococcus aureus, Enterococcus spp, viridans group streptococci, Pseudomonas aeruginosa, and Candida spp. The comparison of TTD values for the two blood culture systems strongly indicated that growth of the first five groups listed above was detected earlier with VIRTUO than with BTA-3D (p < 0.05). The new VIRTUO blood culture system can reduce the TTD for more than 75% of isolated microorganisms. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

A Systematic Review of the Efficacy of Bioactive Compounds in Cardiovascular Disease: Phenolic Compounds

PubMed Central

Rangel-Huerta, Oscar D.; Pastor-Villaescusa, Belen; Aguilera, Concepcion M.; Gil, Angel

2015-01-01

The prevalence of cardiovascular diseases (CVD) is rising and is the prime cause of death in all developed countries. Bioactive compounds (BAC) can have a role in CVD prevention and treatment. The aim of this work was to examine the scientific evidence supporting phenolic BAC efficacy in CVD prevention and treatment by a systematic review. Databases utilized were Medline, LILACS and EMBASE, and all randomized controlled trials (RCTs) with prospective, parallel or crossover designs in humans in which the effects of BAC were compared with that of placebo/control were included. Vascular homeostasis, blood pressure, endothelial function, oxidative stress and inflammatory biomarkers were considered as primary outcomes. Cohort, ecological or case-control studies were not included. We selected 72 articles and verified their quality based on the Scottish Intercollegiate Guidelines Network, establishing diverse quality levels of scientific evidence according to two features: the design and bias risk of a study. Moreover, a grade of recommendation was included, depending on evidence strength of antecedents. Evidence shows that certain polyphenols, such as flavonols can be helpful in decreasing CVD risk factors. However, further rigorous evidence is necessary to support the BAC effect on CVD prevention and treatment. PMID:26132993

A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange.

PubMed

Shi, Xue; Zeng, Haiyang; Xue, Yadong; Luo, Meizhong

2011-10-11

Large-insert BAC and BIBAC libraries are important tools for structural and functional genomics studies of eukaryotic genomes. To facilitate the construction of BAC and BIBAC libraries and the transfer of complete large BAC inserts into BIBAC vectors, which is desired in positional cloning, we developed a pair of new BAC and BIBAC vectors. The new BAC vector pIndigoBAC536-S and the new BIBAC vector BIBAC-S have the following features: 1) both contain two 18-bp non-palindromic I-SceI sites in an inverted orientation at positions that flank an identical DNA fragment containing the lacZ selection marker and the cloning site. Large DNA inserts can be excised from the vectors as single fragments by cutting with I-SceI, allowing the inserts to be easily sized. More importantly, because the two vectors contain different antibiotic resistance genes for transformant selection and produce the same non-complementary 3' protruding ATAA ends by I-SceI that suppress self- and inter-ligations, the exchange of intact large genomic DNA inserts between the BAC and BIBAC vectors is straightforward; 2) both were constructed as high-copy composite vectors. Reliable linearized and dephosphorylated original low-copy pIndigoBAC536-S and BIBAC-S vectors that are ready for library construction can be prepared from the high-copy composite vectors pHZAUBAC1 and pHZAUBIBAC1, respectively, without the need for additional preparation steps or special reagents, thus simplifying the construction of BAC and BIBAC libraries. BIBAC clones constructed with the new BIBAC-S vector are stable in both E. coli and Agrobacterium. The vectors can be accessed through our website http://GResource.hzau.edu.cn. The two new vectors and their respective high-copy composite vectors can largely facilitate the construction and characterization of BAC and BIBAC libraries. The transfer of complete large genomic DNA inserts from one vector to the other is made straightforward.

In Vivo Effects of Preservative-free and Preserved Prostaglandin Analogs: Mouse Ocular Surface Study.

PubMed

Kim, Jee Hyun; Kim, Eun Joo; Kim, Yeoun-Hee; Kim, Yong Il; Lee, Se-Hyung; Jung, Jae-Chang; Lee, Kyoo Won; Park, Young Jeung

2015-08-01

Chronic use of topical hypotensive agents induces several side effects caused by preservatives. The purpose of this study was to evaluate the effects of prostaglandin analogs with varying concentrations of benzalkonium chloride (BAC), preservative-free (PF), and alternative preservatives on mouse corneal tissue. Thirty-five, 8- to 10-week-old female C57BL/6 mice (five mice for each group) were used for this study. To the control group, we applied normal saline, and to each drug-treated group we applied 0.02% BAC, bimatoprost 0.01% (with BAC 0.02%), latanoprost 0.005% (with BAC 0.02%), travoprost 0.004% (with 0.001% polyquad) or tafluprost 0.0015% with/without 0.001% BAC, once a day (9 p.m.) for 4 weeks. Corneal fluorescein staining was evaluated in all groups. After harvest, the corneal tissues were embedded in paraffin and then Hematoxylin-Eosin stain was performed for histopathological examination. Immunofluorescence staining was done against TNF-α, IL-6, HLA DR, pJNK, and pAkt. In corneal fluorescein staining, severe punctate epithelial keratitis was seen in the groups of 0.02% BAC, 0.02% BAC containing bimatoprost 0.01% and latanoprost 0.005%. The surface desquamation, irregular surface, loss of cell borders, anisocytosis and stromal shrinkage were observed in the groups of BAC-containing eye drops. Moreover, the groups treated with BAC-containing eye drops have high inflammatory markers, significantly decreased cell viability-related signal, pAkt, and higher apoptosis-inducing signal, pJNK, than the control group. On the other hand, travoprost 0.004% and PF tafluprost 0.0015% have less cellular morphologic changes, lower inflammation, and higher cellular viability than BAC-containing formulations. Corneal damage, increased inflammation and apoptosis and low cell viability were observed in BAC-containing groups. PF or alternatively preserved glaucoma medications seem to be a reasonable and viable alternative to those preserved with BAC.

In Vivo Effects of Preservative-free and Preserved Prostaglandin Analogs: Mouse Ocular Surface Study

PubMed Central

Kim, Jee Hyun; Kim, Eun Joo; Kim, Yeoun-Hee; Kim, Yong Il; Lee, Se-Hyung; Jung, Jae-Chang; Lee, Kyoo Won

2015-01-01

Purpose Chronic use of topical hypotensive agents induces several side effects caused by preservatives. The purpose of this study was to evaluate the effects of prostaglandin analogs with varying concentrations of benzalkonium chloride (BAC), preservative-free (PF), and alternative preservatives on mouse corneal tissue. Methods Thirty-five, 8- to 10-week-old female C57BL/6 mice (five mice for each group) were used for this study. To the control group, we applied normal saline, and to each drug-treated group we applied 0.02% BAC, bimatoprost 0.01% (with BAC 0.02%), latanoprost 0.005% (with BAC 0.02%), travoprost 0.004% (with 0.001% polyquad) or tafluprost 0.0015% with/without 0.001% BAC, once a day (9 p.m.) for 4 weeks. Corneal fluorescein staining was evaluated in all groups. After harvest, the corneal tissues were embedded in paraffin and then Hematoxylin-Eosin stain was performed for histopathological examination. Immunofluorescence staining was done against TNF-α, IL-6, HLA DR, pJNK, and pAkt. Results In corneal fluorescein staining, severe punctate epithelial keratitis was seen in the groups of 0.02% BAC, 0.02% BAC containing bimatoprost 0.01% and latanoprost 0.005%. The surface desquamation, irregular surface, loss of cell borders, anisocytosis and stromal shrinkage were observed in the groups of BAC-containing eye drops. Moreover, the groups treated with BAC-containing eye drops have high inflammatory markers, significantly decreased cell viability-related signal, pAkt, and higher apoptosis-inducing signal, pJNK, than the control group. On the other hand, travoprost 0.004% and PF tafluprost 0.0015% have less cellular morphologic changes, lower inflammation, and higher cellular viability than BAC-containing formulations. Conclusions Corneal damage, increased inflammation and apoptosis and low cell viability were observed in BAC-containing groups. PF or alternatively preserved glaucoma medications seem to be a reasonable and viable alternative to those preserved with BAC. PMID:26240512

In vitro evaluation of benzalkonium chloride in the preservation of adhesive interfaces.

PubMed

Sabatini, C; Kim, J H; Ortiz Alias, P

2014-01-01

Inhibition of endogenous dentin matrix metalloproteinases (MMPs) by benzalkonium chloride (BAC) decreases collagen solubilization and may help improve resin-dentin bond stability. This study evaluated the resin-dentin bond stability of experimental adhesive blends containing BAC and the stability of dentin matrices by assessing the mass loss and collagen solubilization from dentin beams pretreated with BAC. Twenty-five healthy molars were used for the bond strength evaluation of a two-step etch-and-rinse adhesive (Adper Single Bond Plus, SB) modified with BAC or not. The following groups were tested: 1) SB with no inhibitor (control); 2) topical 2.0% chlorhexidine + SB; 3) 1.0% BAC etchant + SB; 4) 0.5% BAC-SB; and 5) 1.0% BAC-SB. Microtensile bond strength (μTBS) and failure mode distribution under standard error of the mean were evaluated after 24 hours and six months of storage in artificial saliva (AS). A two-way analysis of variance and Tukey test with a significance level of p<0.05 was used for data analysis. In addition, 30 completely demineralized dentin beams from human molars were either dipped in deionized water (DW, control) or dipped in 0.5% and 1.0% BAC for 60 seconds, and then incubated in AS. Collagen solubilization was assessed by evaluating the dry mass loss and quantifying the amount of hydroxyproline (HYP) released from hydrolyzed specimens after four weeks of incubation. The control group demonstrated lower μTBS than some of the experimental groups containing BAC at 24 hours and six months (p<0.05). When BAC was incorporated into the adhesive blend in concentrations of 0.5% and 1.0%, no reduction in dentin bond strength was observed after six months (p<0.05). Less mass loss and HYP release was seen for dentin matrices pretreated with BAC relative to the control pretreated with DW (p<0.05). This in vitro study demonstrates that BAC contributes to the preservation of resin-dentin bonds by reducing collagen degradation.

Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome.

PubMed

Sergeeva, Ekaterina M; Shcherban, Andrey B; Adonina, Irina G; Nesterov, Michail A; Beletsky, Alexey V; Rakitin, Andrey L; Mardanov, Andrey V; Ravin, Nikolai V; Salina, Elena A

2017-11-14

The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat. Three BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70-80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors. A detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread wheat has been established. These two regions differ in the organization of both 5S rDNA and the neighboring sequences comprised of transposable elements, implying different modes of evolution for these regions.

Back to BAC: The Use of Infectious Clone Technologies for Viral Mutagenesis

PubMed Central

Hall, Robyn N.; Meers, Joanne; Fowler, Elizabeth; Mahony, Timothy

2012-01-01

Bacterial artificial chromosome (BAC) vectors were first developed to facilitate the propagation and manipulation of large DNA fragments in molecular biology studies for uses such as genome sequencing projects and genetic disease models. To facilitate these studies, methodologies have been developed to introduce specific mutations that can be directly applied to the mutagenesis of infectious clones (icBAC) using BAC technologies. This has resulted in rapid identification of gene function and expression at unprecedented rates. Here we review the major developments in BAC mutagenesis in vitro. This review summarises the technologies used to construct and introduce mutations into herpesvirus icBAC. It also explores developing technologies likely to provide the next leap in understanding these important viruses. PMID:22470833

Comparative genomics of Lupinus angustifolius gene-rich regions: BAC library exploration, genetic mapping and cytogenetics

PubMed Central

2013-01-01

Background The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume species with a relatively compact genome. The species has 2n = 40 chromosomes and its genome size is 960 Mbp/1C. During the last decade, L. angustifolius genomic studies have achieved several milestones, such as molecular-marker development, linkage maps, and bacterial artificial chromosome (BAC) libraries. Here, these resources were integratively used to identify and sequence two gene-rich regions (GRRs) of the genome. Results The genome was screened with a probe representing the sequence of a microsatellite fragment length polymorphism (MFLP) marker linked to Phomopsis stem blight resistance. BAC clones selected by hybridization were subjected to restriction fingerprinting and contig assembly, and 232 BAC-ends were sequenced and annotated. BAC fluorescence in situ hybridization (BAC-FISH) identified eight single-locus clones. Based on physical mapping, cytogenetic localization, and BAC-end annotation, five clones were chosen for sequencing. Within the sequences of clones that hybridized in FISH to a single-locus, two large GRRs were identified. The GRRs showed strong and conserved synteny to Glycine max duplicated genome regions, illustrated by both identical gene order and parallel orientation. In contrast, in the clones with dispersed FISH signals, more than one-third of sequences were transposable elements. Sequenced, single-locus clones were used to develop 12 genetic markers, increasing the number of L. angustifolius chromosomes linked to appropriate linkage groups by five pairs. Conclusions In general, probes originating from MFLP sequences can assist genome screening and gene discovery. However, such probes are not useful for positional cloning, because they tend to hybridize to numerous loci. GRRs identified in L. angustifolius contained a low number of interspersed repeats and had a high level of synteny to the genome of the model legume G. max. Our results showed that not only was the gene nucleotide sequence conserved between soybean and lupin GRRs, but the order and orientation of particular genes in syntenic blocks was homologous, as well. These findings will be valuable to the forthcoming sequencing of the lupin genome. PMID:23379841

Natural Mutations in Streptococcus agalactiae Resulting in Abrogation of β Antigen Production

PubMed Central

Vasilyeva, Anastasia; Santos Sanches, Ilda; Florindo, Carlos; Dmitriev, Alexander

2015-01-01

Streptococcus agalactiae genome encodes 21 two-component systems (TCS) and a variety of regulatory proteins in order to control gene expression. One of the TCS, BgrRS, comprising the BgrR DNA-binding regulatory protein and BgrS sensor histidine kinase, was discovered within a putative virulence island. BgrRS influences cell metabolism and positively control the expression of bac gene, coding for β antigen at transcriptional level. Inactivation of bgrR abrogated bac gene expression and increased virulence properties of S. agalactiae. In this study, a total of 140 strains were screened for the presence of bac gene, and the TCS bgrR and bgrS genes. A total of 53 strains carried the bac, bgrR and bgrS genes. Most of them (48 strains) expressed β antigen, while five strains did not express β antigen. Three strains, in which bac gene sequence was intact, while bgrR and/or bgrS genes had mutations, and expression of β antigen was absent, were complemented with a constructed plasmid pBgrRS(P) encoding functionally active bgrR and bgrS gene alleles. This procedure restored expression of β antigen indicating the crucial regulatory role of TCS BgrRS. The complemented strain A49V/BgrRS demonstrated attenuated virulence in intraperitoneal mice model of S. agalactiae infection compared to parental strain A49V. In conclusion we showed that disruption of β antigen expression is associated with: i) insertion of ISSa4 upstream the bac gene just after the ribosomal binding site; ii) point mutation G342A resulting a stop codon TGA within the bac gene and a truncated form of β antigen; iii) single deletion (G) in position 439 of the bgrR gene resulting in a frameshift and the loss of DNA-binding domain of the BgrR protein, and iv) single base substitutions in bgrR and bgrS genes causing single amino acid substitutions in BgrR (Arg187Lys) and BgrS (Arg252Gln). The fact that BgrRS negatively controls virulent properties of S. agalactiae gives a novel clue for understanding of S. agalactiae adaptation to the human. PMID:26047354

Natural Mutations in Streptococcus agalactiae Resulting in Abrogation of β Antigen Production.

PubMed

Vasilyeva, Anastasia; Santos Sanches, Ilda; Florindo, Carlos; Dmitriev, Alexander

2015-01-01

Streptococcus agalactiae genome encodes 21 two-component systems (TCS) and a variety of regulatory proteins in order to control gene expression. One of the TCS, BgrRS, comprising the BgrR DNA-binding regulatory protein and BgrS sensor histidine kinase, was discovered within a putative virulence island. BgrRS influences cell metabolism and positively control the expression of bac gene, coding for β antigen at transcriptional level. Inactivation of bgrR abrogated bac gene expression and increased virulence properties of S. agalactiae. In this study, a total of 140 strains were screened for the presence of bac gene, and the TCS bgrR and bgrS genes. A total of 53 strains carried the bac, bgrR and bgrS genes. Most of them (48 strains) expressed β antigen, while five strains did not express β antigen. Three strains, in which bac gene sequence was intact, while bgrR and/or bgrS genes had mutations, and expression of β antigen was absent, were complemented with a constructed plasmid pBgrRS(P) encoding functionally active bgrR and bgrS gene alleles. This procedure restored expression of β antigen indicating the crucial regulatory role of TCS BgrRS. The complemented strain A49V/BgrRS demonstrated attenuated virulence in intraperitoneal mice model of S. agalactiae infection compared to parental strain A49V. In conclusion we showed that disruption of β antigen expression is associated with: i) insertion of ISSa4 upstream the bac gene just after the ribosomal binding site; ii) point mutation G342A resulting a stop codon TGA within the bac gene and a truncated form of β antigen; iii) single deletion (G) in position 439 of the bgrR gene resulting in a frameshift and the loss of DNA-binding domain of the BgrR protein, and iv) single base substitutions in bgrR and bgrS genes causing single amino acid substitutions in BgrR (Arg187Lys) and BgrS (Arg252Gln). The fact that BgrRS negatively controls virulent properties of S. agalactiae gives a novel clue for understanding of S. agalactiae adaptation to the human.

Alcohol consumption decreases lactate clearance in acutely injured patients☆

PubMed Central

Dezman, Zachary D.W.; Comer, Angela C.; Narayan, Mayur; Scalea, Thomas M.; Hirshon, Jon Mark; Smith, Gordon S.

2017-01-01

Introduction Alcohol, a common risk factor for injury, has direct toxic effects on the liver. The use of lactate clearance has been well described as an indicator of the adequacy of resuscitation in injured patients. We investigated whether acutely injured patients with positive blood alcohol content (+BAC) had less lactate clearance than sober patients. Methods We conducted a retrospective cohort study of acutely injured patients treated at an urban Level 1 trauma centre between January 2010 and December 2012. Blood alcohol and venous lactate levels were measured on all patients at the time of arrival. Study subjects were patients transported directly from the scene of injury, who had an elevated lactate concentration on arrival (≥3.0 mmol/L) and at least one subsequent lactate measurement within 24 h after admission. Lactate clearance ([Lactate1 − Lactate2]/Lactate1) was calculated for all patients. Chi-squared tests were used to compare values from sober and intoxicated subjects. Lactate clearance was plotted against alcohol levels and stratified by age and Injury Severity Score (ISS). Results Serial lactate concentration measurements were obtained in 3910 patients; 1674 of them had +BAC. Patients with +BAC were younger (mean age: 36.6 [SD 14.7] vs 41.0 [SD 19.9] years [p = 0.0001]), were more often male (83.4% vs 75.9% [p = 0.0001]), had more minor injuries (ISS < 9) (33.8% vs 27.1% [p = 0.0001]), had a lower in-hospital mortality rate (1.4% vs 3.9% [p = 0.0001]), but also had lower average lactate clearance (37.8% vs 47.6% [p = 0.0001]). The lactate clearance of the sober patients (47.6 [SD 33.5]) was twice that of those with +BAC >400 (23.5 [SD 6.5]). Lactate clearance decreased with increasing BAC irrespective of age and ISS. Conclusions In a large group of acutely injured patients, a dose-dependent decrease in lactate clearance was seen in those with elevated BAC. This relationship will cause a falsely elevated lactate reading or prolong lactate clearance and should be taken into account when evaluating patients with +BAC. PMID:27025567

Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

PubMed

Seoane-Zonjic, Pedro; Cañas, Rafael A; Bautista, Rocío; Gómez-Maldonado, Josefa; Arrillaga, Isabel; Fernández-Pozo, Noé; Claros, M Gonzalo; Cánovas, Francisco M; Ávila, Concepción

2016-02-27

In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82% of the gene structures, and a high proportion (85%) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members. The experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a Ruby gem for this class of analyses.

An evaluation of three processing methods and the effect of reduced culture times for faster direct identification of pathogens from BacT/ALERT blood cultures by MALDI-TOF MS.

PubMed

Loonen, A J M; Jansz, A R; Stalpers, J; Wolffs, P F G; van den Brule, A J C

2012-07-01

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is a fast and reliable method for the identification of bacteria from agar media. Direct identification from positive blood cultures should decrease the time to obtaining the result. In this study, three different processing methods for the rapid direct identification of bacteria from positive blood culture bottles were compared. In total, 101 positive aerobe BacT/ALERT bottles were included in this study. Aliquots from all bottles were used for three bacterial processing methods, i.e. the commercially available Bruker's MALDI Sepsityper kit, the commercially available Molzym's MolYsis Basic5 kit and a centrifugation/washing method. In addition, the best method was used to evaluate the possibility of MALDI application after a reduced incubation time of 7 h of Staphylococcus aureus- and Escherichia coli-spiked (1,000, 100 and 10 colony-forming units [CFU]) aerobe BacT/ALERT blood cultures. Sixty-six (65%), 51 (50.5%) and 79 (78%) bottles were identified correctly at the species level when the centrifugation/washing method, MolYsis Basic 5 and Sepsityper were used, respectively. Incorrect identification was obtained in 35 (35%), 50 (49.5%) and 22 (22%) bottles, respectively. Gram-positive cocci were correctly identified in 33/52 (64%) of the cases. However, Gram-negative rods showed a correct identification in 45/47 (96%) of all bottles when the Sepsityper kit was used. Seven hours of pre-incubation of S. aureus- and E. coli-spiked aerobe BacT/ALERT blood cultures never resulted in reliable identification with MALDI-TOF MS. Sepsityper is superior for the direct identification of microorganisms from aerobe BacT/ALERT bottles. Gram-negative pathogens show better results compared to Gram-positive bacteria. Reduced incubation followed by MALDI-TOF MS did not result in faster reliable identification.

Ecotoxicity of disinfectant benzalkonium chloride and its mixture with antineoplastic drug 5-fluorouracil towards alga Pseudokirchneriella subcapitata

PubMed Central

Ženko, Maja

2018-01-01

Background Benzalkonium chloride (BAC) is one of the most common ingredients of the disinfectants. It is commonly detected in surface and wastewaters where it can interact with the residues of pharmaceuticals that are also common wastewater pollutants. Among the latter, the residues of antineoplastic drugs are of particular concern as recent studies showed that they can induce adverse effect in aquatic organisms at environmentally relevant concentrations. Methods Ecotoxicity of BAC as an individual compound and in a binary mixture with an antineoplastic drug 5-fluorouracil (5-FU) was determined towards alga Pseudokirchneriella subcapitata, a representative of primary producers. The toxicity of the BAC+5-FU binary mixture was predicted by the two basic models: concentration addition (CA) and independent action (IA), and compared to the experimentally determined toxicity. Additionally combination index (CI) was calculated to determine the type of interaction. Results After 72 h exposure to BAC a concentration dependent growth inhibition of P. subcapitata was observed with an EC50 0.255 mg/L. Comparing the predicted no effect concentration to the measured concentrations in the surface waters indicate that BAC at current applications and occurrence in aquatic environment may affect algal populations. The measured toxicity of the mixture was higher from the predicted and calculated CI confirmed synergistic effect on the inhibition of algal growth, at least at EC50 concentration. The observed synergism may have impact on the overall toxicity of wastewaters, whereas it is less likely for general environments because the concentrations of 5-FU are several orders of magnitude lower from its predicted no effect concentration. Discussion These results indicate that combined effects of mixtures of disinfectants and antineoplastic drugs should be considered in particular when dealing with environmental risk assessment as well as the management of municipal and hospital wastewaters. PMID:29938131

Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malouli, Daniel; Nakayasu, Ernesto S.; Viswanathan, Kasinath

2012-09-01

Cytomegaloviruses are highly host restricted resulting in co-speciation with their hosts. As a natural pathogen of rhesus macaques (RM), Rhesus Cytomegalovirus (RhCMV) has therefore emerged as a highly relevant experimental model for pathogenesis and vaccine development due to its close evolutionary relationship to human CMV (HCMV). To date, most in vivo experiments performed with RhCMV employed strain 68-1 cloned as bacterial artificial chromosome (BAC). However, the complete genome sequence of the 68-1 BAC has not been determined. Furthermore, the gene content of the RhCMV genome is unknown and previous open reading frame (ORF) predictions relied solely on uninterrupted ORFs withmore » an arbitrary cutoff of 300bp. To obtain a more precise picture of the actual proteins encoded by the most commonly used molecular clone of RhCMV we re-evaluated the RhCMV 68-1 BAC-genome by whole genome shotgun sequencing and determined the protein content of the resulting RhCMV virions by proteomics. By additionally comparing the RhCMV genome to that of several closely related Old World Monkey (OWM) CMVs we were able to filter out many unlikely ORFs and obtain a simplified map of the RhCMV genome. This comparative genomics analysis eliminated many genes previously characterized as RhCMV-specific while consolidating a high conservation of ORFs among OWM-CMVs and between RhCMV and HCMV. Moreover, virion proteomics independently validated the revised ORF predictions since only proteins encoded by predicted ORFs could be detected. Taken together these data suggest a much higher conservation of genome and virion structure between CMVs of humans, apes and OWMs than previously assumed. Remarkably, BAC-derived RhCMV is able to establish and maintain persistent infection despite the lack of multiple genes homologous to HCMV genes involved in tissue tropism.« less

Collegiate-based emergency medical service: impact on alcohol-related emergency department transports at a small liberal arts college.

PubMed

Rosen, Joshua B; Olson, Mark H; Kelly, Marianne

2012-01-01

The authors examined the impact of a collegiate-based emergency medical service (CBEMS) on the frequency of emergency department (ED) transports. Students transported to the ED for acute alcohol intoxication during the Fall 2008 and the Fall 2009 semesters (N = 50). The frequency of students receiving transportation to a hospital ED and the reported blood alcohol content (BAC) levels during the initial operational semester of the CBEMS were compared to those values over the same time period the previous year. More than twice the number of students was transported to the ED following the introduction of CBEMS. There was no change in mean BAC levels. CBEMS could promote a culture conducive to increased reporting behavior, which makes the campus safer. Similar BAC levels suggest that the degree of intoxication was similar for the 2 reporting periods, but students sought emergency assistance more frequently following the inception of CBEMS.

A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere

PubMed Central

Sumer, Huseyin; Craig, Jeffrey M.; Sibson, Mandy; Choo, K.H. Andy

2003-01-01

Human neocentromeres are fully functional centromeres that arise at previously noncentromeric regions of the genome. We have tested a rapid procedure of genomic array analysis of chromosome scaffold/matrix attachment regions (S/MARs), involving the isolation of S/MAR DNA and hybridization of this DNA to a genomic BAC/PAC array. Using this procedure, we have defined a 2.5-Mb domain of S/MAR-enriched chromatin that fully encompasses a previously mapped centromere protein-A (CENP-A)-associated domain at a human neocentromere. We have independently verified this procedure using a previously established fluorescence in situ hybridization method on salt-treated metaphase chromosomes. In silico sequence analysis of the S/MAR-enriched and surrounding regions has revealed no outstanding sequence-related predisposition. This study defines the S/MAR-enriched domain of a higher eukaryotic centromere and provides a method that has broad application for the mapping of S/MAR attachment sites over large genomic regions or throughout a genome. PMID:12840048

Investigation of decolorization of textile wastewater in an anaerobic/aerobic biological activated carbon system (A/A BAC).

PubMed

Pasukphun, N; Vinitnantharat, S; Gheewala, S

2010-04-01

The aim of this study is to investigate the decolorization in anaerobic/aerobic biological activated carbon (A/A BAC) system. The experiment was divided into 2 stages; stage I is batch test for preliminary study of dye removal equilibrium time. The preliminary experiment (stage I) provided the optimal data for experimental design of A/A BAC system in SBR (stage II). Stage II is A/A BAC system imitated Sequencing Batch Reactor (SBR) which consist of 5 main periods; fill, react, settle, draw and idle. React period include anaerobic phase followed by aerobic phase. The BAC main media; Granular Activated Carbon (GAC), Mixed Cultures (MC) and Biological Activated Carbon (BAC) were used for dye and organic substances removal in three different solutions; Desizing Agent Solution (DAS), dye Solution (DS) and Synthetic Textile Wastewater (STW). Results indicate that GAC adsorption plays role in dye removal followed by BAC and MC activities, respectively. In the presence desizing agent, decolorization by MC was improved because desizing agent acts as co-substrates for microorganisms. It was found that 50% of dye removal efficiency was achieved in Fill period by MC. GC/MS analysis was used to identify dye intermediate from decolorization. Dye intermediate containing amine group was found in the solution and on BAC surfaces. The results demonstrated that combination of MC and BAC in the system promotes decolorization and dye intermediate removal. In order to improve dye removal efficiency in an A/A BAC system, replacement of virgin GAC, sufficient co-substrates supply and the appropriate anaerobic: aerobic period should be considered.

The anti-MMP activity of benzalkonium chloride

PubMed Central

Tezvergil-Mutluay, Arzu; Mutluay, M. Murat; Gu, Li-sha; Zhang, Kai; Agee, Kelli A.; Carvalho, Ricardo M.; Manso, Adriana; Carrilho, Marcela; Tay, Franklin R.; Breschi, Lorenzo; Suh, Byoung-In; Pashley, David H.

2013-01-01

SUMMARY Objective This study evaluated the ability of benzalkonium chloride (BAC) to bind to dentine and to inhibit soluble recombinant MMPs and bound dentine matrix metalloproteinases (MMPs). Methods Dentine powder was prepared from extracted human molars. Half was left mineralized; the other half was completely demineralized. The binding of BAC to dentine powder was followed by measuring changes in the supernatant concentration using UV spectrometry. The inhibitory effects of BAC on rhMMP-2, -8 and -9 were followed using a commercially available in vitro proteolytic assay. Matrix-bound endogenous MMP-activity was evaluated in completely demineralized beams. Each beam was either dipped into BAC and then dropped into 1 mL of a complete medium (CM) or they were placed in 1 mL of CM containing BAC for 30 d. After 30 d, changes in the dry mass of the beams or in the hydroxyproline (HYP) content of hydrolyzates of the media were quantitated as indirect measures of matrix collagen hydrolysis by MMPs. Results Demineralized dentine powder took up 10-times more BAC than did mineralized powder. Water rinsing removed about 50% of the bound BAC, while rinsing with 0.5 M NaCl removed more than 90% of the bound BAC. BAC concentrations 0.5 wt% produced 100% inhibition of soluble recombinant MMP-2, -8 or -9, and inhibited matrix-bound MMPs between 55-66% when measured as mass loss or 76-81% when measured as solubilization of collagen peptide fragments. Conclusions BAC is effective at inhibiting both soluble recombinant MMPs and matrix-bound dentine MMPs in the absence of resins. PMID:20951183

Validation of the Persian version of the brief assessment of cognition in schizophrenia in patients with schizophrenia and healthy controls.

PubMed

Mazhari, Shahrzad; Parvaresh, Nooshin; Eslami Shahrbabaki, Mahin; Sadeghi, Mohammad M; Nakhaee, Nouzar; Keefe, Richard S E

2014-02-01

The Brief Assessment of Cognition in Schizophrenia (BACS) is designed for assessment of cognitive function in patients with schizophrenia. Versions of the BACS in English and other languages have been shown to be as sensitive to cognitive dysfunction as a standard test battery, with the advantage of brief administration and scoring time. The present study aimed to test the concurrent validity of the Persian version of the BACS (Persian-BACS). A group of 50 patients with schizophrenia-spectrum disorders and a group of 50 healthy controls received the Persian-BACS in a first session, and in a second session a standard neurocognitive battery. Cronbach's alpha for the Persian-BACS was 0.74. All the Persian-BACS subscales were significantly correlated with the corresponding standard neurocognitive subscales and the Pearson correlation of the composite scores from the two instruments was 0.71. Moreover, a one-factor solution was found that accounted for 67.9% of the variance. Finally, the Persian-BACS demonstrated high ability to discriminate patients with schizophrenia from healthy controls. Good psychometric properties of the Persian-BACS suggest that it is a useful tool for assessing cognition in schizophrenic patients with Persian as their primary language. © 2013 The Authors. Psychiatry and Clinical Neurosciences © 2013 Japanese Society of Psychiatry and Neurology.

Breast Arterial Calcification Is Associated with Reproductive Factors in Asymptomatic Postmenopausal Women

PubMed Central

Whaley, Dana H.; Sheedy, Patrick F.; Peyser, Patricia A.

2010-01-01

Abstract Objective The etiology of breast arterial calcification (BAC) is not well understood. We examined reproductive history and cardiovascular disease (CVD) risk factor associations with the presence of detectable BAC in asymptomatic postmenopausal women. Methods Reproductive history and CVD risk factors were obtained in 240 asymptomatic postmenopausal women from a community-based research study who had a screening mammogram within 2 years of their participation in the study. The mammograms were reviewed for the presence of detectable BAC. Age-adjusted logistic regression models were fit to assess the association between each risk factor and the presence of BAC. Multiple variable logistic regression models were used to identify the most parsimonious model for the presence of BAC. Results The prevalence of BAC increased with increased age (p < 0.0001). The most parsimonious logistic regression model for BAC presence included age at time of examination, increased parity (p = 0.01), earlier age at first birth (p = 0.002), weight, and an age-by-weight interaction term (p = 0.004). Older women with a smaller body size had a higher probability of having BAC than women of the same age with a larger body size. Conclusions The presence or absence of BAC at mammography may provide an assessment of a postmenopausal woman's lifetime estrogen exposure and indicate women who could be at risk for hormonally related conditions. PMID:20629578

Physical Mapping in a Triplicated Genome: Mapping the Downy Mildew Resistance Locus Pp523 in Brassica oleracea L.

PubMed Central

Carlier, Jorge D.; Alabaça, Claudia S.; Sousa, Nelson H.; Coelho, Paula S.; Monteiro, António A.; Paterson, Andrew H.; Leitão, José M.

2011-01-01

We describe the construction of a BAC contig and identification of a minimal tiling path that encompass the dominant and monogenically inherited downy mildew resistance locus Pp523 of Brassica oleracea L. The selection of BAC clones for construction of the physical map was carried out by screening gridded BAC libraries with DNA overgo probes derived from both genetically mapped DNA markers flanking the locus of interest and BAC-end sequences that align to Arabidopsis thaliana sequences within the previously identified syntenic region. The selected BAC clones consistently mapped to three different genomic regions of B. oleracea. Although 83 BAC clones were accurately mapped within a ∼4.6 cM region surrounding the downy mildew resistance locus Pp523, a subset of 33 BAC clones mapped to another region on chromosome C8 that was ∼60 cM away from the resistance gene, and a subset of 63 BAC clones mapped to chromosome C5. These results reflect the triplication of the Brassica genomes since their divergence from a common ancestor shared with A. thaliana, and they are consonant with recent analyses of the C genome of Brassica napus. The assembly of a minimal tiling path constituted by 13 (BoT01) BAC clones that span the Pp523 locus sets the stage for map-based cloning of this resistance gene. PMID:22384370

Comparison of BacT/Alert FAN and FAN Plus Bottles with Conventional Medium for Culturing Cerebrospinal Fluid.

PubMed

Yoo, In Young; Chun, Sejong; Song, Dong Joon; Huh, Hee Jae; Lee, Nam Yong

2016-11-01

We compared the BacT/Alert system FAN and FAN Plus media to conventional media for culturing cerebrospinal fluid (CSF) with 2,545 samples. FAN/FAN Plus bottles showed better performance for isolating microorganisms in CSF than conventional media (positive rate, 7.2% [182/2,545] versus 3.1% [80/2,545]). The incremental recovery rate of Cryptococcus neoformans from FAN Plus bottles was higher than that from FAN bottles. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping

USDA-ARS?s Scientific Manuscript database

A bacterial artificial chromosome (BAC) library and BAC-end sequences for Gossypium hirsutum L. have recently been developed. Here we report on genomic-based genome-wide SNP mining utilizing re-sequencing data with a BAC-end sequence reference for twelve G. hirsutum L. lines, one G. barbadense L. li...

Design and Fabrication of a Tank-Applied Broad Area Cooling Shield Coupon

NASA Technical Reports Server (NTRS)

Wood, J. J.; Middlemas, M. R.

2012-01-01

The small-scale broad area cooling (BAC) shield test panel represents a section of the cryogenic propellant storage and transfer ground test article, a flight-like cryogenic propellant storage tank. The test panel design includes an aluminum tank shell, primer, spray-on foam insulation, multilayer insulation (MLI), and BAC shield hardware. This assembly was sized to accurately represent the character of the MLI/BAC shield system, be quickly and inexpensively assembled, and be tested in the Marshall Space Flight Center Acoustic Test Facility. Investigating the BAC shield response to a worst-case launch dynamic load was the key purpose for developing the test article and performing the test. A preliminary method for structurally supporting the BAC shield using low-conductivity standoffs was designed, manufactured, and evaluated as part of the test. The BAC tube-standoff interface and unsupported BAC tube lengths were key parameters for evaluation. No noticeable damage to any system hardware element was observed after acoustic testing.

Hybrid process of BAC and sMBR for treating polluted raw water.

PubMed

Tian, Jia-yu; Chen, Zhong-lin; Yang, Yan-ling; Liang, Heng; Nan, Jun; Wang, Zhao-zhi; Li, Gui-bai

2009-12-01

The hybrid process of biological activated carbon (BAC) and submerged membrane bioreactor (sMBR) was evaluated for the drinking water treatment from polluted raw water, with the respective hydraulic retention time of 0.5 h. The results confirmed the synergetic effects between the BAC and the subsequent sMBR. A moderate amount of ammonium (54.5%) was decreased in the BAC; while the total removal efficiency was increased to 89.8% after the further treatment by the sMBR. In the hybrid process, adsorption of granular activated carbon (in BAC), two stages of biodegradation (in BAC and sMBR), and separation by the membrane (in sMBR) jointly contributed to the removal of organic matter. As a result, the hybrid process managed to eliminate influent DOC, UV(254), COD(Mn), TOC, BDOC and AOC by 26.3%, 29.9%, 22.8%, 27.8%, 57.2% and 49.3%, respectively. Due to the pre-treatment effect of BAC, the membrane fouling in the downstream sMBR was substantially mitigated.

Topical timolol with and without benzalkonium chloride: epithelial permeability and autofluorescence of the cornea in glaucoma.

PubMed

de Jong, C; Stolwijk, T; Kuppens, E; de Keizer, R; van Best, J

1994-04-01

Epithelial permeability and autofluorescence of the cornea were determined by fluorophotometry in 21 patients with open-angle glaucoma or ocular hypertension using timolol medication with the preservative benzalkonium chloride (BAC) and 2 weeks after changing to timolol medication without BAC. The investigation was performed to determine whether removal of BAC would reduce toxic effects on the cornea and complaints of sensations of burning or dry eye. Corneal epithelial permeability decreased significantly after changing medication (mean decrease per patient 27%, P = 0.025). Corneal autofluorescence increased significantly after changing medication suggesting an alteration in corneal metabolism (mean increase per patient 6%, P = 0.003). Timolol without BAC was found to be as effective as timolol with BAC in reducing intraocular pressure (P = 0.4). Removal of BAC from timolol resulted in an improvement of corneal epithelial barrier function and in a reduction of complaints. The improvement was found to be proportional to the duration of the preceding BAC-containing therapy.

Deviation from expected cognitive ability across psychotic disorders.

PubMed

Hochberger, W C; Combs, T; Reilly, J L; Bishop, J R; Keefe, R S E; Clementz, B A; Keshavan, M S; Pearlson, G D; Tamminga, C A; Hill, S K; Sweeney, J A

2018-02-01

Patients with schizophrenia show a deficit in cognitive ability compared to estimated premorbid and familial intellectual abilities. However, the degree to which this pattern holds across psychotic disorders and is familial is unclear. The present study examined deviation from expected cognitive level in schizophrenia, schizoaffective disorder, and psychotic bipolar disorder probands and their first-degree relatives. Using a norm-based regression approach, parental education and WRAT-IV Reading scores (both significant predictors of cognitive level in the healthy control group) were used to predict global neuropsychological function as measured by the composite score from the Brief Assessment of Cognition in Schizophrenia (BACS) test in probands and relatives. When compared to healthy control group, psychotic probands showed a significant gap between observed and predicted BACS composite scores and a greater likelihood of robust cognitive decline. This effect was not seen in unaffected relatives. While BACS and WRAT-IV Reading scores were themselves highly familial, the decline in cognitive function from expectation had lower estimates of familiality. Thus, illness-related factors such as epigenetic, treatment, or pathophysiological factors may be important causes of illness related decline in cognitive abilities across psychotic disorders. This is consistent with the markedly greater level of cognitive impairment seen in affected individuals compared to their unaffected family members. Copyright © 2017 Elsevier B.V. All rights reserved.

[Operative treatment and remote results in patients with bronchoalveolar lung cancer].

PubMed

Uchikov, A; Batashki, I; Dimitrov, I; Uchikova, E; Belovezhdov, V; Bonev, P

2008-01-01

Bronchoalveolar pulmonary carcinoma (BAC) is a type of adenocarcinoma with an increasing frequency. Because BAC rarely metastasize outside the thorax, the postoperative results are good. We present 28 patients with BAC, operated in the clinic for a period of 7 years--12 patients with an infiltrative form of BAC, 16 patients with nodular form 12 patients underwent lobectomy, 15 patients--pneumonectomy, and 1 patient--bilobectomy. The 5-years-survival rate is 50%. We found a better 5-years survival rate for the patients with BAC in comparison with the other histological types of non-small cell pulmonary carcinoma

Variations in biofilm formation, desiccation resistance and Benzalkonium chloride susceptibility among Listeria monocytogenes strains isolated in Canada.

PubMed

Piercey, Marta J; Ells, Timothy C; Macintosh, Andrew J; Truelstrup Hansen, Lisbeth

2017-09-18

Listeria monocytogenes is a pathogenic foodborne microorganism noted for its ability to survive in the environment and food processing facilities. Survival may be related to the phenotype of individual strains including the ability to form biofilms and resist desiccation and/or sanitizer exposure. The objectives of this research were to compare 14 L. monocytogenes strains isolated from blood (3), food (6) and water (5) with respect to their benzalkonium chloride (BAC) sensitivity, desiccation resistance, and ability to form biofilm. Correlations were tested between those responses, and the presence of the SSI-1 (Stress Survival Islet) and LGI1/CC8 (Listeria Genomic Island 1 in a clonal complex 8 background) genetic markers. Genetic sequences from four strains representing different phenotypes were also probed for predicted amino acid differences in biofilm, desiccation, and membrane related genes. The water isolates were among the most desiccation susceptible strains, while strains exhibiting desiccation resistance harboured SSI-1 or both the SSI-1 and LGI1/CC8 markers. BAC resistance was greatest in planktonic LGI1/CC8 cells (relative to non-LGI1/CC8 cells), and higher BAC concentrations were also needed to inhibit the formation of biofilm by LGI1/CC8 strains during incubation for 48h and 6days compared to other strains. Formation of biofilm on stainless steel was not significantly (p>0.05) different among the strains. Analysis of genetic sequence data from desiccation and BAC sensitive (CP4 5-1, CP5 2-3, both from water), intermediate (Lm568, food) and desiccation and BAC resistant (08 5578, blood, human outbreak) strains led to the finding of amino acid differences in predicted functional protein domains in several biofilm, desiccation and peptidoglycan related genes (e.g., lmo0263, lmo0433, lmo0434, lmo0771, lmo0973, lmo1080, lmo1224, lmo1370, lmo1744, and lmo2558). Notably, the LGI1/CC8 strain 08-5578 had a frameshift mutation in lmo1370, a gene previously associated with desiccation resistance. In conclusion, the more desiccation and BAC resistant LGI1/CC8 isolates may pose a challenge for sanitation efforts. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme.

PubMed

Cowell, John K; Matsui, Sei-Ichi; Wang, Yong D; LaDuca, Jeffrey; Conroy, Jeffrey; McQuaid, Devin; Nowak, Norma J

2004-05-01

Identification of genetic losses and gains is valuable in analysis of brain tumors. Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci. These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells. Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than 1 MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment. These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region. Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested. We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa. Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa. In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies. There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample. CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture. CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells. This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence. CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads.

Chromosome Rearrangements in Cornelia de Lange Syndrome (CdLS): Report of a der(3)t(3;12)(p25.3;p13.3) in Two Half Sibs With Features of CdLS and Review of Reported CdLS Cases With Chromosome Rearrangements

PubMed Central

DeScipio, Cheryl; Kaur, Maninder; Yaeger, Dinah; Innis, Jeffrey W.; Spinner, Nancy B.; Jackson, Laird G.; Krantz, Ian D.

2016-01-01

Cornelia de Lange syndrome (CdLS; OMIM 122470) is a dominantly inherited disorder characterized by multisystem involvement, cognitive delay, limb defects, and characteristic facial features. Recently, mutations in NIPBL have been found in ~50% of individuals with CdLS. Numerous chromosomal rearrangements have been reported in individuals with CdLS. These rearrangements may be causative of a CdLS phenotype, result in a phenocopy, or be unrelated to the observed phenotype. We describe two half siblings with a der(3)t(3;12)(p25.3;p13.3) chromosomal rearrangement, clinical features resembling CdLS, and phenotypic overlap with the del(3)(p25) phenotype. Region-specific BAC probes were used to fine-map the breakpoint region by fluorescence in situ hybridization (FISH). FISH analysis places the chromosome 3 breakpoint distal to RP11-115G3 on 3p25.3; the chromosome 12 breakpoint is distal to BAC RP11-88D16 on 12p13.3. A review of published cases of terminal 3p deletions and terminal 12p duplications indicates that the findings in these siblings are consistent with the del(3)(p25) phenotype. Given the phenotypic overlap with CdLS, we have reviewed the reported cases of chromosomal rearrangements involved in CdLS to better elucidate other potential loci that could harbor additional CdLS genes. Additionally, to identify chromosome rearrangements, genome-wide array comparative genomic hybridization (CGH) was performed on eight individuals with typical CdLS and without identifiable deletion or mutation of NIPBL. No pathologic rearrangements were identified. PMID:16075459

Official blame for drivers with very low blood alcohol content: there is no safe combination of drinking and driving.

PubMed

Phillips, David P; Sousa, Ana Luiza R; Moshfegh, Rebecca T

2015-04-01

Some laboratory studies find that driving is impaired even at blood alcohol content (BAC)=0.01%. However, no real-world traffic studies have investigated whether minimally 'buzzed' drivers (BAC=0.01%) are more likely to be blamed for a crash than are the sober drivers they collide with. To determine whether official blame for a crash increases significantly at BAC=0.01%. We examined the relationship between the driver's BAC and the degree to which he or she was assigned sole official blame (SOB) for the crash. We analysed an official, exhaustive, nationwide US database (Fatality Analysis Reporting System; n=570 731), covering 1994-2011. Even minimally 'buzzed' drivers are 46% (24-72%) more likely to be officially blamed for a crash than are the sober drivers they collide with (χ(2)=20.45; p=0.000006). There is no threshold effect-no sudden transition from blameless to blamed drivers at BAC=0.08% (the US legal limit). Instead, SOB increases smoothly and strongly with BAC (r=0.98 (0.96-0.99) for male drivers, p<0.000001; r=0.99 (0.97-0.99) for female drivers, p<0.000001). This near-linear SOB-to-BAC relationship begins at BAC=0.01% and ends around BAC=0.24%. Our findings persist after controlling for many confounding variables. There appears to be no safe combination of drinking and driving-even minimally 'buzzed' drivers pose increased risk to themselves and to others. Concerns about drunk driving should also be extended to 'buzzed' driving. US legislators should reduce the legal BAC limit, perhaps to 0.05%, as in most European countries. Lowering the legal BAC limit is likely to reduce injuries and save lives. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simon, M. I.; Kim, U.-J.

We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping andmore » sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year.« less

Anchoring 9,371 Maize Expressed Sequence Tagged Unigenes to the Bacterial Artificial Chromosome Contig Map by Two-Dimensional Overgo Hybridization1

PubMed Central

Gardiner, Jack; Schroeder, Steven; Polacco, Mary L.; Sanchez-Villeda, Hector; Fang, Zhiwei; Morgante, Michele; Landewe, Tim; Fengler, Kevin; Useche, Francisco; Hanafey, Michael; Tingey, Scott; Chou, Hugh; Wing, Rod; Soderlund, Carol; Coe, Edward H.

2004-01-01

Our goal is to construct a robust physical map for maize (Zea mays) comprehensively integrated with the genetic map. We have used a two-dimensional 24 × 24 overgo pooling strategy to anchor maize expressed sequence tagged (EST) unigenes to 165,888 bacterial artificial chromosomes (BACs) on high-density filters. A set of 70,716 public maize ESTs seeded derivation of 10,723 EST unigene assemblies. From these assemblies, 10,642 overgo sequences of 40 bp were applied as hybridization probes. BAC addresses were obtained for 9,371 overgo probes, representing an 88% success rate. More than 96% of the successful overgo probes identified two or more BACs, while 5% identified more than 50 BACs. The majority of BACs identified (79%) were hybridized with one or two overgos. A small number of BACs hybridized with eight or more overgos, suggesting that these BACs must be gene rich. Approximately 5,670 overgos identified BACs assembled within one contig, indicating that these probes are highly locus specific. A total of 1,795 megabases (Mb; 87%) of the total 2,050 Mb in BAC contigs were associated with one or more overgos, which are serving as sequence-tagged sites for single nucleotide polymorphism development. Overgo density ranged from less than one overgo per megabase to greater than 20 overgos per megabase. The majority of contigs (52%) hit by overgos contained three to nine overgos per megabase. Analysis of approximately 1,022 Mb of genetically anchored BAC contigs indicates that 9,003 of the total 13,900 overgo-contig sites are genetically anchored. Our results indicate overgos are a powerful approach for generating gene-specific hybridization probes that are facilitating the assembly of an integrated genetic and physical map for maize. PMID:15020742

Using phone sensors and an artificial neural network to detect gait changes during drinking episodes in the natural environment.

PubMed

Suffoletto, Brian; Gharani, Pedram; Chung, Tammy; Karimi, Hassan

2018-02-01

Phone sensors could be useful in assessing changes in gait that occur with alcohol consumption. This study determined (1) feasibility of collecting gait-related data during drinking occasions in the natural environment, and (2) how gait-related features measured by phone sensors relate to estimated blood alcohol concentration (eBAC). Ten young adult heavy drinkers were prompted to complete a 5-step gait task every hour from 8pm to 12am over four consecutive weekends. We collected 3-axis accelerometer, gyroscope, and magnetometer data from phone sensors, and computed 24 gait-related features using a sliding window technique. eBAC levels were calculated at each time point based on Ecological Momentary Assessment (EMA) of alcohol use. We used an artificial neural network model to analyze associations between sensor features and eBACs in training (70% of the data) and validation and test (30% of the data) datasets. We analyzed 128 data points where both eBAC and gait-related sensor data were captured, either when not drinking (n=60), while eBAC was ascending (n=55) or eBAC was descending (n=13). 21 data points were captured at times when the eBAC was greater than the legal limit (0.08mg/dl). Using a Bayesian regularized neural network, gait-related phone sensor features showed a high correlation with eBAC (Pearson's r>0.9), and >95% of estimated eBAC would fall between -0.012 and +0.012 of actual eBAC. It is feasible to collect gait-related data from smartphone sensors during drinking occasions in the natural environment. Sensor-based features can be used to infer gait changes associated with elevated blood alcohol content. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling correction of severe urea cycle defects in the growing murine liver using a hybrid recombinant adeno-associated virus/piggyBac transposase gene delivery system.

PubMed

Cunningham, Sharon C; Siew, Susan M; Hallwirth, Claus V; Bolitho, Christine; Sasaki, Natsuki; Garg, Gagan; Michael, Iacovos P; Hetherington, Nicola A; Carpenter, Kevin; de Alencastro, Gustavo; Nagy, Andras; Alexander, Ian E

2015-08-01

Liver-targeted gene therapy based on recombinant adeno-associated viral vectors (rAAV) shows promising therapeutic efficacy in animal models and adult-focused clinical trials. This promise, however, is not directly translatable to the growing liver, where high rates of hepatocellular proliferation are accompanied by loss of episomal rAAV genomes and subsequently a loss in therapeutic efficacy. We have developed a hybrid rAAV/piggyBac transposon vector system combining the highly efficient liver-targeting properties of rAAV with stable piggyBac-mediated transposition of the transgene into the hepatocyte genome. Transposition efficiency was first tested using an enhanced green fluorescent protein expression cassette following delivery to newborn wild-type mice, with a 20-fold increase in stably gene-modified hepatocytes observed 4 weeks posttreatment compared to traditional rAAV gene delivery. We next modeled the therapeutic potential of the system in the context of severe urea cycle defects. A single treatment in the perinatal period was sufficient to confer robust and stable phenotype correction in the ornithine transcarbamylase-deficient Spf(ash) mouse and the neonatal lethal argininosuccinate synthetase knockout mouse. Finally, transposon integration patterns were analyzed, revealing 127,386 unique integration sites which conformed to previously published piggyBac data. Using a hybrid rAAV/piggyBac transposon vector system, we achieved stable therapeutic protection in two urea cycle defect mouse models; a clinically conceivable early application of this technology in the management of severe urea cycle defects could be as a bridging therapy while awaiting liver transplantation; further improvement of the system will result from the development of highly human liver-tropic capsids, the use of alternative strategies to achieve transient transposase expression, and engineered refinements in the safety profile of piggyBac transposase-mediated integration. © 2015 by the American Association for the Study of Liver Diseases.

A first generation BAC-based physical map of the rainbow trout genome

PubMed Central

Palti, Yniv; Luo, Ming-Cheng; Hu, Yuqin; Genet, Carine; You, Frank M; Vallejo, Roger L; Thorgaard, Gary H; Wheeler, Paul A; Rexroad, Caird E

2009-01-01

Background Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species. Results The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map. Conclusion The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of QTL, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of MAS into rainbow trout breeding programs. PMID:19814815

Fatally injured pedestrians and bicyclists in the United States with high blood alcohol concentrations.

PubMed

Eichelberger, Angela H; McCartt, Anne T; Cicchino, Jessica B

2018-06-01

Little research has focused on the problem of alcohol impairment among pedestrians and bicyclists in the United States. The aim of the current study was to investigate the prevalence, trends, and characteristics of alcohol-impaired fatally injured pedestrians and bicyclists. Data from the Fatality Analysis Reporting System (FARS) were analyzed for fatally injured passenger vehicle drivers, pedestrians, and bicyclists 16 and older during 1982-2014. Logistic regression models examined whether personal, roadway, and crash characteristics were associated with high blood alcohol concentrations (BACs) among fatally injured pedestrians and bicyclists. From 1982 to 2014, the percentage of fatally injured pedestrians with high BACs (≥0.08g/dL) declined from 45% to 35%, and the percentage of fatally injured bicyclists with high BACs declined from 28% to 21%. By comparison, the percentage of fatally injured passenger vehicle drivers with high BACs declined from 51% in 1982 to 32% in 2014. The largest reductions in alcohol impairment among fatally injured pedestrians and bicyclists were found among ages 16-20. During 2010-2014, fatally injured pedestrians and bicyclists ages 40-49 had the highest odds of having a high BAC, compared with other age groups. A substantial proportion of fatally injured pedestrians and bicyclists have high BACs, and this proportion has declined less dramatically than for fatally injured passenger vehicle drivers during the past three decades. Most countermeasures used to address alcohol-impaired driving may have only limited effectiveness in reducing fatalities among alcohol-impaired pedestrians and bicyclists. Efforts should increase public awareness of the risk of walking or bicycling when impaired. Results suggest the primary target audience for educational campaigns directed at pedestrians and bicyclists is middle-age males. Further research should evaluate the effectiveness of potential countermeasures, such as lowering speeds or improving lighting in urban areas. Copyright © 2018 National Safety Council and Elsevier Ltd. All rights reserved.

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

PubMed Central

2011-01-01

Background One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. Results The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. Conclusions This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak. PMID:21645357

A Microplate Growth Inhibition Assay for Screening Bacteriocins against Listeria monocytogenes to Differentiate Their Mode-of-Action.

PubMed

Vijayakumar, Paul Priyesh; Muriana, Peter M

2015-06-11

Lactic acid bacteria (LAB) have historically been used in food fermentations to preserve foods and are generally-recognized-as-safe (GRAS) by the FDA for use as food ingredients. In addition to lactic acid; some strains also produce bacteriocins that have been proposed for use as food preservatives. In this study we examined the inhibition of Listeria monocytogenes 39-2 by neutralized and non-neutralized bacteriocin preparations (Bac+ preps) produced by Lactobacillus curvatus FS47; Lb. curvatus Beef3; Pediococcus acidilactici Bac3; Lactococcus lactis FLS1; Enterococcus faecium FS56-1; and Enterococcus thailandicus FS92. Activity differences between non-neutralized and neutralized Bac+ preps in agar spot assays could not readily be attributed to acid because a bacteriocin-negative control strain was not inhibitory to Listeria in these assays. When neutralized and non-neutralized Bac+ preps were used in microplate growth inhibition assays against L. monocytogenes 39-2 we observed some differences attributed to acid inhibition. A microplate growth inhibition assay was used to compare inhibitory reactions of wild-type and bacteriocin-resistant variants of L. monocytogenes to differentiate bacteriocins with different modes-of-action (MOA) whereby curvaticins FS47 and Beef3, and pediocin Bac3 were categorized to be in MOA1; enterocins FS92 and FS56-1 in MOA2; and lacticin FLS1 in MOA3. The microplate bacteriocin MOA assay establishes a platform to evaluate the best combination of bacteriocin preparations for use in food applications as biopreservatives against L. monocytogenes.

Effects of Acute Alcohol Tolerance on Perceptions of Danger and Willingness to Drive after Drinking

PubMed Central

Amlung, Michael T.; Morris, David H.; McCarthy, Denis M.

2014-01-01

Rationale Drinking and driving is associated with elevated rates of motor vehicle accidents and fatalities. Previous research suggests that alcohol impairs judgments about the dangers of risky behaviors; however, how alcohol affects driving-related judgments is less clear. Impairments have also been shown to differ across limbs of the blood alcohol concentration (BAC) curve, which is known as acute tolerance. Objectives Examine whether perceptions about the dangerousness of driving after drinking and willingness to drive differed across ascending and descending limbs of the BAC curve. Test whether reductions in perceived danger were associated with willingness to drive on the descending limb. Methods Fifty-six participants were randomly assigned to receive either a moderate dose of alcohol (peak BAC = 0.10 g%) or placebo. We assessed perceived dangerousness and willingness to drive at matched BACs (~0.067-0.068 g%) on the ascending and descending limbs. Results Both perceived danger and willingness to drive showed acute tolerance in the alcohol group. Participants judged driving to be significantly less dangerous and were more willing to drive on the descending limb compared to the ascending limb. The magnitude of change in perceived danger significantly predicted willingness to drive on the descending limb. Conclusions Decreased impairment associated with acute tolerance may lead individuals to underestimate the dangerousness of driving after drinking and in turn make poor decisions regarding driving. This study further emphasizes the descending limb as a period of increased risk and offers support for enhancing prevention efforts by targeting drivers at declining BAC levels. PMID:24752657

Chromosomal Mapping of Canine-Derived BAC Clones to the Red Fox and American Mink Genomes

PubMed Central

Vorobieva, Nadegda V.; Beklemisheva, Violetta R.; Johnson, Jennifer L.; Temnykh, Svetlana V.; Yudkin, Dmitry V.; Trut, Lyudmila N.; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D.; Acland, Gregory M.; Graphodatsky, Alexander S.

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene–containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations. PMID:19546120

[Ru/AC catalyzed ozonation of recalcitrant organic compounds].

PubMed

Wang, Jian-Bing; Hou, Shao-Pei; Zhou, Yun-Rui; Zhu, Wan-Peng; He, Xu-Wen

2009-09-15

Ozonation and Ru/AC catalyzed ozonation of dimethyl phthalate (DMP), phenols and disinfection by-products precursors were studied. It shows that Ru/AC catalyst can obviously enhance the mineralization of organic compounds. In the degradation of DMP, TOC removal was 28.84% by ozonation alone while it was 66.13% by catalytic ozonation. In the oxidation of 23 kinds of phenols, TOC removals were 9.57%-56.08% by ozonation alone while they were 41.81%-82.32% by catalytic ozonation. Compared to ozonation alone, Ru/AC catalyzed ozonation was more effective for the reduction of disinfection by-products formation potentials in source water. The reduction of haloacetic acids formation potentials was more obvious than thichlomethane formation potentials. After the treatment by catalytic ozonation, the haloacetic acids formation potentials decreased from 144.02 microg/L to 58.50 microg/L, which was below the standard value of EPA. However ozonation alone could not make it reach the standard. The treatments of source water by BAC, O3 + BAC, O3/AC + BAC and Ru/AC + O3 + BAC were also studied. In the four processes, TOC removal was 3.80%, 20.14%, 27.45% and 48.30% respectively, COD removal was 4.37%, 27.22%, 39.91% and 50.00% respectively, UV254 removal was 8.16%, 62.24%, 67.03% and 84.95% respectively. Ru/AC + O3 + BAC process is more effective than the other processes for the removal of TOC, COD and UV254 and no ruthenium leaching observed in the solution. It is a promising process for the treatment of micro polluted source water.

Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes.

PubMed

Kukekova, Anna V; Vorobieva, Nadegda V; Beklemisheva, Violetta R; Johnson, Jennifer L; Temnykh, Svetlana V; Yudkin, Dmitry V; Trut, Lyudmila N; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D; Acland, Gregory M; Graphodatsky, Alexander S

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.

A rabbit dry eye model induced by topical medication of a preservative benzalkonium chloride.

PubMed

Xiong, Cuiju; Chen, Dong; Liu, Jingbo; Liu, Bingqian; Li, Naiyang; Zhou, Yang; Liang, Xuanwei; Ma, Ping; Ye, Chengtian; Ge, Jian; Wang, Zhichong

2008-05-01

To establish a rabbit dry eye model with topical medication of the ocular preparation preservative benzalkonium chloride (BAC). Sixteen white rabbits were used. One eye of each rabbit was chosen randomly for topical administration of 0.1% BAC twice daily for 14 days. The other untreated eyes served as controls. Schirmer test, fluorescein, and rose bengal staining were performed before and after BAC treatment on days 3, 5, 7, and 14. Conjunctiva impression cytology specimens were collected on days 0, 7, and 14. The rabbits were killed after day 14. Immunofluorescence staining was performed to detect mucin-5 subtype AC (MUC5AC) on conjunctival cryosections. Cornea and conjunctiva structures were evaluated by light and electron microscopy. Compared with untreated controls, BAC-treated eyes showed significant decreases in Schirmer scores (P = 0.01) and increases in fluorescein scores (P < 0.001) on days 5, 7, and 14. A significant increase in rose bengal scores was noticed as early as day 3 (P = 0.001). Decreases in goblet cell density occurred on days 7 and 14 (P = 0.001). Decreased MUC5AC and histopathologic and ultrastructural disorders of the cornea and conjunctiva were also observed in the BAC group. These findings demonstrated that an ophthalmic preservative, benzalkonium chloride, induced a dry eye syndrome in rabbits with damage to the cornea and conjunctiva, decreased aqueous tear basal secretion, goblet cell loss, and MUC5AC deficiency. This rabbit model was consistent with human dry eye syndrome in both aqueous tear and mucin deficiency and may be appropriate for studying dry eye syndrome.

A Microplate Growth Inhibition Assay for Screening Bacteriocins against Listeria monocytogenes to Differentiate Their Mode-of-Action

PubMed Central

Vijayakumar, Paul Priyesh; Muriana, Peter M.

2015-01-01

Lactic acid bacteria (LAB) have historically been used in food fermentations to preserve foods and are generally-recognized-as-safe (GRAS) by the FDA for use as food ingredients. In addition to lactic acid; some strains also produce bacteriocins that have been proposed for use as food preservatives. In this study we examined the inhibition of Listeria monocytogenes 39-2 by neutralized and non-neutralized bacteriocin preparations (Bac+ preps) produced by Lactobacillus curvatus FS47; Lb. curvatus Beef3; Pediococcus acidilactici Bac3; Lactococcus lactis FLS1; Enterococcus faecium FS56-1; and Enterococcus thailandicus FS92. Activity differences between non-neutralized and neutralized Bac+ preps in agar spot assays could not readily be attributed to acid because a bacteriocin-negative control strain was not inhibitory to Listeria in these assays. When neutralized and non-neutralized Bac+ preps were used in microplate growth inhibition assays against L. monocytogenes 39-2 we observed some differences attributed to acid inhibition. A microplate growth inhibition assay was used to compare inhibitory reactions of wild-type and bacteriocin-resistant variants of L. monocytogenes to differentiate bacteriocins with different modes-of-action (MOA) whereby curvaticins FS47 and Beef3, and pediocin Bac3 were categorized to be in MOA1; enterocins FS92 and FS56-1 in MOA2; and lacticin FLS1 in MOA3. The microplate bacteriocin MOA assay establishes a platform to evaluate the best combination of bacteriocin preparations for use in food applications as biopreservatives against L. monocytogenes. PMID:26111195

[Characteristic of the removal of 2,4-dichlorophenol by biological activated carbon].

PubMed

Liu, Hong; Li, An-jie; Quan, Xiang-chun; Kong, Xiang-hui; Yun, Ying

2004-11-01

The adsorption characteristics and kinetics of 2,4-Dichlorophenol (2,4-DCP) by biological activated carbon (BAC) was studied through contrast experiments with conventional activated sludge alone or quartz as the carrier. The advantage and disadvantage of removing 2,4-DCP using BAC and the mechanism of this process were investigated. The results show that the method of removing 2,4-DCP by BAC is applicable in practices, and the process of BAC demonstrates high removal rate than the process of suspended activated sludge and biofilm with quartz as the carrier. In addition, the BAC process showed high resistance to shock loadings, therefore, it is suitable to be utilized at high organic loading and under long-term operation. In BAC-system, activated carbon could not only adsorb 2,4-DCP but also oxidized 2,4-DCP.

Mechanism and toxicity research of benzalkonium chloride oxidation in aqueous solution by H2O2/Fe(2+) process.

PubMed

Zhang, Qian; Xia, Yu-Feng; Hong, Jun-Ming

2016-09-01

As widely used disinfectants, the pollution caused by benzalkonium chloride (BAC) has attracted a lot of attention in recent years. Since it is not suitable for biodegradation, BAC was degraded firstly by Fenton advanced oxidation technologies (AOTs) in this research to enhance the biodegradability of the pollutions. The result revealed that the optimal molar ratio of H2O2/Fe(2+) for BAC degradation was 10:1, and the COD removal rate was 32 %. To clarify the pathway of degradation, the technique of GC-MS was implemented herein to identify intermediates and the toxicity of those BAC intermediates were also novelty tested through microbial fuel cells (MFC). The findings indicated that ten transformation products including benzyl dimethyl amine and dodecane were formed during the H2O2/Fe(2+) processes, which means the degradation pathway of BAC was initiated both on the hydrophobic (alkyl chain) and hydrophilic (benzyl and ammonium moiety) region of the surfactant. The toxicity of BAC before and after treated by Fenton process was monitored through MFC system. The electricity generation was improved 337 % after BAC was treated by H2O2/Fe(2+) oxidation processes which indicated that the toxicity of those intermediates were much lower than BAC. The mechanism and toxicity research in this paper could provide the in-depth understanding to the pathway of BAC degradation and proved the possibility of AOTs for the pretreatment of a biodegradation process.

A review: Potential and challenges of biologically activated carbon to remove natural organic matter in drinking water purification process.

PubMed

Korotta-Gamage, Shashika Madushi; Sathasivan, Arumugam

2017-01-01

The use of biologically activated carbon (BAC) in drinking water purification is reviewed. In the past BAC is seen mostly as a polishing treatment. However, BAC has the potential to provide solution to recent challenges faced by water utilities arising from change in natural organic matter (NOM) composition in drinking water sources - increased NOM concentration with a larger fraction of hydrophilic compounds and ever increasing trace level organic pollutants. Hydrophilic NOM is not removed by traditional coagulation process and causes bacterial regrowth and increases disinfection by-products (DBPs) formation during disinfection. BAC can offer many advantages by removing hydrophilic fraction and many toxic and endocrine compounds which are not otherwise removed. BAC can also aid the other downstream processes if used as a pre-treatment. Major drawback of BAC was longer empty bed contact time (EBCT) required for an effective NOM removal. This critical review analyses the strategies that have been adopted to enhance the biological activity of the carbon by operational means and summarises the surface modification methods. To maximize the benefit of the BAC, a rethink of current treatment plant configuration is proposed. If the process can be expedited and adopted appropriately, BAC can solve many of the current problems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Drivers who self-estimate lower blood alcohol concentrations are riskier drivers after drinking.

PubMed

Laude, Jennifer R; Fillmore, Mark T

2016-04-01

Alcohol increases the tendency for risky driving in some individuals but not others. Little is known about the factors underlying this individual difference. Studies find that those who underestimate their blood alcohol concentration (BAC) following a dose of alcohol tend to be more impulsive and report greater willingness to drive after drinking than those who estimate their BACs to be greater than their actual BAC. BAC underestimation could contribute to risky driving behavior following alcohol as such drivers might perceive little impairment in their driving ability and thus no need for caution. This study was designed to test the relationship between drivers' BAC estimations following a dose of alcohol or a placebo and the degree of risky driving they displayed during a simulated driving test. Forty adult drivers performed a simulated driving test and estimated their blood alcohol concentration after receiving a dose of alcohol (0.65 g/kg for men and 0.56 g/kg for women) or a placebo. Alcohol increased risk-taking and impaired driving skill. Those who estimated their BAC to be lower were the riskiest drivers following both alcohol and placebo. The tendency to estimate lower BACs could support a series of high-risk decisions, regardless of one's actual BAC. This could include the decision to drive after drinking.

Abnormalities of mental rotation of hands associated with speed of information processing and executive function in chronic schizophrenic patients.

PubMed

Mazhari, Shahrzad; Moghadas Tabrizi, Yousef

2014-06-01

Deficits in mental imagery ability have been reported in patients with schizophrenia. However, there is scarce evidence about the correlation between impairment in mental rotation and other cognitive deficits in the patients. The aim of this study was to assess mental rotation ability, along with other measures of cognitive function in patients with schizophrenia. The performance of 29 patients with schizophrenia was compared with 29 healthy controls. Mental rotation was measured with the Hand Rotation Task, and cognitive functions were measured with the Brief Assessment of Cognition in Schizophrenia (BACS). On Hand Rotation Task, the patients were significantly slower and less accurate compared to controls. Moreover, mental rotation accuracy was significantly correlated with all the BACS domains except verbal memory. In multiple regression analysis, the two BACS subscales, Tower of London and Symbol Coding tasks, were significant predictors and accounted for 41% of the variance in accuracy in the patients. These results support previous findings showing dysfunction of the posterior parietal cortex in schizophrenia, which is involved in general mental rotation, as well as other cognitive processes. © 2014 The Authors. Psychiatry and Clinical Neurosciences © 2014 Japanese Society of Psychiatry and Neurology.

Nucleic acid stains as indicators of Giardia muris viability following cyst inactivation.

PubMed

Taghi-Kilani, R; Gyürék, L L; Millard, P J; Finch, G R; Belosevic, M

1996-06-01

A reliable viability assay for Giardia is required for the development of disinfection process design criteria and pathogen monitoring by water treatment utilities. Surveys of single-staining nucleic acid dyes (stain dead parasites only), and double-staining vital dye kits from Molecular Probes (stain live and dead parasites) were conducted to assess the viability of untreated, heat-killed, and chemically inactivated Giardia muris cysts. Nucleic acid staining results were compared to those of in vitro excystation and animal infectivity. Nucleic acid stain, designated as SYTO-9, was considered the best among the single-staining dyes for its ability to stain dead cysts brightly and its relatively slow decay rate of visible light emission following DNA binding. SYTO-9 staining was correlated to animal infectivity. A Live/Dead BacLight was found to be the better of 2 double-staining viability kits tested. Logarithmic survival ratios based on SYTO-9 and Live/Dead BacLight were compared to excystation and infectivity results for G. muris cysts exposed to ozone or free chlorine. The results indicate that SYTO-9 and Live/Dead BacLight staining is stable following treatment of cysts with chemical disinfectants.

Biodegradation of persistent organics can overcome adsorption-desorption hysteresis in biological activated carbon systems.

PubMed

Abromaitis, V; Racys, V; van der Marel, P; Meulepas, R J W

2016-04-01

In Biological Activated Carbon (BAC) systems, persistent organic pollutants can be removed through a combination of adsorption, desorption and biodegradation. These processes might be affected by the presence of other organics, especially by the more abundant easily-biodegradable organics, like acetate. In this research these relations are quantified for the removal of the persistent pharmaceutical metoprolol. Acetate did not affect the adsorption and desorption of metoprolol, but it did greatly enhance the metoprolol biodegradation. At least part of the BAC biomass growing on acetate was also able to metabolise metoprolol, although metoprolol was only converted after the acetate was depleted. The presence of easily-degradable organics like acetate in the feeding water is therefore beneficial for the removal of metoprolol in BAC systems. The isotherms obtained from metoprolol adsorption and desorption experiments showed that BAC systems are subject to hysteresis; for AC bioregeneration to take place the microbial biomass has to reduce the concentration at the AC-biomass interface 2.7 times compared to the concentration at which the carbon was being loaded. However, given the threshold concentration of the MET degrading microorganisms (<0.08 μg/L) versus the average influent concentration (1.3 μg/L), bioregeneration is feasible. Copyright © 2016 Elsevier Ltd. All rights reserved.

A peptide factor secreted by Staphylococcus pseudintermedius exhibits properties of both bacteriocins and virulence factors.

PubMed

Wladyka, Benedykt; Piejko, Marcin; Bzowska, Monika; Pieta, Piotr; Krzysik, Monika; Mazurek, Łukasz; Guevara-Lora, Ibeth; Bukowski, Michał; Sabat, Artur J; Friedrich, Alexander W; Bonar, Emilia; Międzobrodzki, Jacek; Dubin, Adam; Mak, Paweł

2015-09-28

Staphylococcus pseudintermedius is a common commensal bacterium colonizing the skin and mucosal surfaces of household animals. However, it has recently emerged as a dangerous opportunistic pathogen, comparable to S. aureus for humans. The epidemiological situation is further complicated by the increasing number of methicillin-resistant S. pseudintermedius infections and evidence of gene transmission driving antibiotic resistance between staphylococci colonizing human and zoonotic hosts. In the present study, we describe a unique peptide, BacSp222, that possesses features characteristic of both bacteriocins and virulence factors. BacSp222 is secreted in high quantities by S. pseudintermedius strain 222 isolated from dog skin lesions. This linear, fifty-amino-acid highly cationic peptide is plasmid-encoded and does not exhibit significant sequence similarities to any other known peptides or proteins. BacSp222 kills gram-positive bacteria (at doses ranging from 0.1 to several micromol/l) but also demonstrates significant cytotoxic activities towards eukaryotic cells at slightly higher concentrations. Moreover, at nanomolar concentrations, the peptide also possesses modulatory properties, efficiently enhancing interferon gamma-induced nitric oxide release in murine macrophage-like cell lines. BacSp222 appears to be one of the first examples of multifunctional peptides that breaks the convention of splitting bacteriocins and virulence factors into two unrelated groups.

A peptide factor secreted by Staphylococcus pseudintermedius exhibits properties of both bacteriocins and virulence factors

PubMed Central

Wladyka, Benedykt; Piejko, Marcin; Bzowska, Monika; Pieta, Piotr; Krzysik, Monika; Mazurek, Łukasz; Guevara-Lora, Ibeth; Bukowski, Michał; Sabat, Artur J.; Friedrich, Alexander W.; Bonar, Emilia; Międzobrodzki, Jacek; Dubin, Adam; Mak, Paweł

2015-01-01

Staphylococcus pseudintermedius is a common commensal bacterium colonizing the skin and mucosal surfaces of household animals. However, it has recently emerged as a dangerous opportunistic pathogen, comparable to S. aureus for humans. The epidemiological situation is further complicated by the increasing number of methicillin-resistant S. pseudintermedius infections and evidence of gene transmission driving antibiotic resistance between staphylococci colonizing human and zoonotic hosts. In the present study, we describe a unique peptide, BacSp222, that possesses features characteristic of both bacteriocins and virulence factors. BacSp222 is secreted in high quantities by S. pseudintermedius strain 222 isolated from dog skin lesions. This linear, fifty-amino-acid highly cationic peptide is plasmid-encoded and does not exhibit significant sequence similarities to any other known peptides or proteins. BacSp222 kills gram-positive bacteria (at doses ranging from 0.1 to several micromol/l) but also demonstrates significant cytotoxic activities towards eukaryotic cells at slightly higher concentrations. Moreover, at nanomolar concentrations, the peptide also possesses modulatory properties, efficiently enhancing interferon gamma-induced nitric oxide release in murine macrophage-like cell lines. BacSp222 appears to be one of the first examples of multifunctional peptides that breaks the convention of splitting bacteriocins and virulence factors into two unrelated groups. PMID:26411997

Preparation and characterization of N-benzoyl-O-acetyl-chitosan.

PubMed

Cai, Jinping; Dang, Qifeng; Liu, Chengsheng; Fan, Bing; Yan, Jingquan; Xu, Yanyan; Li, Jingjing

2015-01-01

A novel amphipathic chitosan derivative, N-benzoyl-O-acetyl-chitosan (BACS), was prepared by using the selective partial acylation of chitosan (CS), benzoyl chloride, and acetic acid under high-intensity ultrasound. The chemical structure and physical properties of BACS were characterized by FTIR, (1)H NMR, TGA, and XRD techniques. The degrees of substitution of benzoyl and acetyl for the chitosan derivatives were 0.26 and 1.15, respectively, which were calculated from the peak areas in NMR spectra by using the combined integral methods. The foaming properties of CS and BACS were determined and the results suggested BACS had better foam capacity and stability than those of chitosan. In addition, the antimicrobial activities of CS and BACS were also investigated against two species of bacteria (Escherichia coli and Staphylococcus aureus) and a fungus (Aspergillus niger), the results indicated that the antibacterial and antifungal activities of BACS were much stronger than those of the parent chitosan. These findings suggested that BACS was preferable for use as a food additive with a dual role of both foaming agent and food preservative. Copyright © 2015 Elsevier B.V. All rights reserved.

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6

PubMed Central

2011-01-01

Background The fermented dried seeds of Theobroma cacao (cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected. Results Here, we describe the construction of a BAC-based integrated genetic-physical map of the T. cacao cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the two T. cacao cultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed. Conclusions The results presented in this study are a stand-alone resource for functional exploitation and enhancement of Theobroma cacao but are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of the T. cacao genome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays. PMID:21846342

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6.

PubMed

Saski, Christopher A; Feltus, Frank A; Staton, Margaret E; Blackmon, Barbara P; Ficklin, Stephen P; Kuhn, David N; Schnell, Raymond J; Shapiro, Howard; Motamayor, Juan Carlos

2011-08-16

The fermented dried seeds of Theobroma cacao (cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected. Here, we describe the construction of a BAC-based integrated genetic-physical map of the T. cacao cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the two T. cacao cultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed. The results presented in this study are a stand-alone resource for functional exploitation and enhancement of Theobroma cacao but are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of the T. cacao genome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.

Self-Estimation of Blood Alcohol Concentration: A Review

PubMed Central

Aston, Elizabeth R.; Liguori, Anthony

2013-01-01

This article reviews the history of blood alcohol concentration (BAC) estimation training, which trains drinkers to discriminate distinct BAC levels and thus avoid excessive alcohol consumption. BAC estimation training typically combines education concerning alcohol metabolism with attention to subjective internal cues associated with specific concentrations. Estimation training was originally conceived as a component of controlled drinking programs. However, dependent drinkers were unsuccessful in BAC estimation, likely due to extreme tolerance. In contrast, moderate drinkers successfully acquired this ability. A subsequent line of research translated laboratory estimation studies to naturalistic settings by studying large samples of drinkers in their preferred drinking environments. Thus far, naturalistic studies have provided mixed results regarding the most effective form of BAC feedback. BAC estimation training is important because it imparts an ability to perceive individualized impairment that may be present below the legal limit for driving. Consequently, the training can be a useful component for moderate drinkers in drunk driving prevention programs. PMID:23380489

Bronchioloalveolar carcinoma.

PubMed

Arenberg, Douglas

2011-02-01

This review focuses on aspects of bronchioloalveolar carcinoma (BAC) in which it differs importantly from other forms of non-small-cell lung cancer. BAC is a form of adenocarcinoma with unique clinical, radiological, and epidemiological features. With the notable exception of a lower likelihood of a positive positron-emission tomographic (PET) scan in BAC, staging, diagnosis, and treatment are largely the same as for other histological subtypes of lung cancer. However, additional treatment options exist that are equivalent, if not more effective, for many patients with BAC. The diagnosis of BAC should be reserved for those tumors meeting the 1999/2004 criteria set forth by the World Health Organization. Revised nomenclature proposed by an expert consensus panel may change how this disease is viewed. Additional clinical trials are needed on patients with BAC, employing strict definitions and enrollment criteria to allow the results to be applied to appropriate patient populations. © Thieme Medical Publishers.

In vitro effects of preserved and unpreserved anti-allergic drugs on human corneal epithelial cells.

PubMed

Guzman-Aranguez, Ana; Calvo, Patricia; Ropero, Inés; Pintor, Jesús

2014-11-01

Treatment with topical eye drops for long-standing ocular diseases like allergy can induce detrimental side effects. The purpose of this study was to investigate in vitro cytotoxicity of commercially preserved and unpreserved anti-allergic eye drops on the viability and barrier function of monolayer and stratified human corneal-limbal epithelial cells. Cells were treated with unpreserved ketotifen solution, benzalkonium chloride (BAC)-containing anti-allergic drugs (ketotifen, olopatadine, levocabastine) as well as BAC alone. 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay was used to determine cell viability. Effects of compounds on barrier function were analyzed measuring transepithelial electrical resistance (TEER) to determine paracellular permeability and rose bengal assays to evaluate transcellular barrier formation. The BAC-preserved anti-allergic formulations and BAC alone significantly reduced cell viability, monolayer cultures being more sensitive to damage by these solutions. Unpreserved ketotifen induced the least diminution in cell viability. The extent of decrease of cell viability was clearly dependent of BAC presence, but it was also affected by the different types of drugs when the concentration of BAC was low and the short time of exposure. Treatment with BAC-containing anti-allergic drugs and BAC alone resulted in increased paracellular permeability and loss of transcellular barrier function as indicated by TEER measurement and rose bengal assays. The presence of the preservative BAC in anti-allergic eye drop formulations contributes importantly to the cytotoxic effects induced by these compounds. Stratified cell cultures seem to be a more relevant model for toxicity evaluation induced on the ocular surface epithelia than monolayer cultures.

Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

PubMed Central

2012-01-01

Background Bread wheat, one of the world’s staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC) is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS) for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat. Results The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA) generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes) and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4%) was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR) and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE) and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from 758 SSRs and 695 Insertion Site Based Polymorphisms (ISBPs). Of the 96 ISBP primer pairs tested, 28 (29%) were 3A-specific and compared to 17 (18%) for 96 SSRs. Conclusion This work reports on the use of wheat chromosome arm 3AS-specific BAC library for the targeted generation of sequence data from a particular region of the huge genome of wheat. A large quantity of sequences were generated from the A genome of hexaploid wheat for comparative genome analysis with homoeologous B and D genomes and other model grass genomes. Hundreds of molecular markers were developed from the 3AS arm-specific sequences; these and other sequences will be useful in gene discovery and physical mapping. PMID:22559868

Alcohol in fatal recreational boating accidents

DOT National Transportation Integrated Search

1988-05-01

Data on the blood alcohol concentration (BAC) of fatal recreational boating accident : victims were assembled for four states with reasonably good reporting on BAC between : 1980 and 1985. In all there were data on BAC for 370 dead boaters. Of these ...

Blood Alcohol Concentration-Related Lower Performance in Immediate Visual Memory and Working Memory in Adolescent Binge Drinkers

PubMed Central

Vinader-Caerols, Concepción; Duque, Aránzazu; Montañés, Adriana; Monleón, Santiago

2017-01-01

The binge drinking (BD) pattern of alcohol consumption is prevalent during adolescence, a period characterized by critical changes to the structural and functional development of brain areas related with memory and cognition. There is considerable evidence of the cognitive dysfunctions caused by the neurotoxic effects of BD in the not-yet-adult brain. Thus, the aim of the present study was to evaluate the effects of different blood alcohol concentrations (BAC) on memory during late adolescence (18–19 years old) in males and females with a history of BD. The sample consisted of 154 adolescents (67 males and 87 females) that were classified as refrainers if they had never previously drunk alcoholic drinks and as binge drinkers if they had drunk six or more standard drink units in a row for men or five or more for women at a minimum frequency of three occasions in a month, throughout the previous 12 months. After intake of a high acute dose of alcohol by binge drinkers or a control refreshment by refrainers and binge drinkers, subjects were distributed into four groups for each gender according to their BAC: BAC0-R (0 g/L, in refrainers), BAC0-BD (0 g/L, in binge drinkers), BAC1 (0.3 – 0.5 g/L, in binge drinkers) or BAC2 (0.54 – 1.1 g/L, in binge drinkers). The subjects’ immediate visual memory and working memory were then measured according to the Wechsler Memory Scale (WMS-III). The BAC1 group showed lower scores of immediate visual memory but not of working memory, while lower performance in both memories were found in the BAC2 group. Therefore, the brain of binge drinkers with moderate BAC could be employing compensatory mechanisms from additional brain areas to perform a working memory task adequately, but these resources would be undermined when BAC is higher (>0.5 g/L). No gender differences were found in BAC-related lower performance in immediate visual memory and working memory. In conclusion, immediate visual memory is more sensitive than working memory to the neurotoxic effects of alcohol in adolescent binge drinkers of both genders, being a BAC-related lower performance, and without obvious differences between males and females. PMID:29046656

Blood Alcohol Concentration-Related Lower Performance in Immediate Visual Memory and Working Memory in Adolescent Binge Drinkers.

PubMed

Vinader-Caerols, Concepción; Duque, Aránzazu; Montañés, Adriana; Monleón, Santiago

2017-01-01

The binge drinking (BD) pattern of alcohol consumption is prevalent during adolescence, a period characterized by critical changes to the structural and functional development of brain areas related with memory and cognition. There is considerable evidence of the cognitive dysfunctions caused by the neurotoxic effects of BD in the not-yet-adult brain. Thus, the aim of the present study was to evaluate the effects of different blood alcohol concentrations (BAC) on memory during late adolescence (18-19 years old) in males and females with a history of BD. The sample consisted of 154 adolescents (67 males and 87 females) that were classified as refrainers if they had never previously drunk alcoholic drinks and as binge drinkers if they had drunk six or more standard drink units in a row for men or five or more for women at a minimum frequency of three occasions in a month, throughout the previous 12 months. After intake of a high acute dose of alcohol by binge drinkers or a control refreshment by refrainers and binge drinkers, subjects were distributed into four groups for each gender according to their BAC: BAC0-R (0 g/L, in refrainers), BAC0-BD (0 g/L, in binge drinkers), BAC1 (0.3 - 0.5 g/L, in binge drinkers) or BAC2 (0.54 - 1.1 g/L, in binge drinkers). The subjects' immediate visual memory and working memory were then measured according to the Wechsler Memory Scale (WMS-III). The BAC1 group showed lower scores of immediate visual memory but not of working memory, while lower performance in both memories were found in the BAC2 group. Therefore, the brain of binge drinkers with moderate BAC could be employing compensatory mechanisms from additional brain areas to perform a working memory task adequately, but these resources would be undermined when BAC is higher (>0.5 g/L). No gender differences were found in BAC-related lower performance in immediate visual memory and working memory. In conclusion, immediate visual memory is more sensitive than working memory to the neurotoxic effects of alcohol in adolescent binge drinkers of both genders, being a BAC-related lower performance, and without obvious differences between males and females.

Autism-specific copy number variants further implicate the phosphatidylinositol signaling pathway and the glutamatergic synapse in the etiology of the disorder

PubMed Central

Cuscó, Ivon; Medrano, Andrés; Gener, Blanca; Vilardell, Mireia; Gallastegui, Fátima; Villa, Olaya; González, Eva; Rodríguez-Santiago, Benjamín; Vilella, Elisabet; Del Campo, Miguel; Pérez-Jurado, Luis A.

2009-01-01

Autism spectrum disorders (ASDs) constitute a group of severe neurodevelopmental conditions with complex multifactorial etiology. In order to explore the hypothesis that submicroscopic genomic rearrangements underlie some ASD cases, we have analyzed 96 Spanish patients with idiopathic ASD after extensive clinical and laboratory screening, by array comparative genomic hybridization (aCGH) using a homemade bacterial artificial chromosome (BAC) array. Only 13 of the 238 detected copy number alterations, ranging in size from 89 kb to 2.4 Mb, were present specifically in the autistic population (12 out of 96 individuals, 12.5%). Following validation by additional molecular techniques, we have characterized these novel candidate regions containing 24 different genes including alterations in two previously reported regions of chromosome 7 associated with the ASD phenotype. Some of the genes located in ASD-specific copy number variants act in common pathways, most notably the phosphatidylinositol signaling and the glutamatergic synapse, both known to be affected in several genetic syndromes related with autism and previously associated with ASD. Our work supports the idea that the functional alteration of genes in related neuronal networks is involved in the etiology of the ASD phenotype and confirms a significant diagnostic yield for aCGH, which should probably be included in the diagnostic workup of idiopathic ASD. PMID:19246517

Bronchoalveolar carcinoma: current treatment and future trends.

PubMed

Laskin, Janessa J

2004-12-01

Bronchoalveolar carcinoma (BAC) is a subtype of non-small-cell lung cancer (NSCLC) with unique clinical and pathologic characteristics. The most recent classification system defines BAC as a primary lung cancer that tends to be peripheral and grow in a lepedic fashion along the alveolar septae without parenchymal invasion. Most of the clinical information on BAC comes from retrospective institutional reviews; however, recent studies have focused more specifically on BAC. In particular, clinical trials of molecular-targeted anticancer therapies against the epidermal growth factor receptor have led to a deeper understanding of the distinct features of this cancer and suggest that BAC may require a therapeutic paradigm different from that of other NSCLCs.

Drivers who self-estimate lower blood alcohol concentrations are riskier drivers after drinking

PubMed Central

Laude, Jennifer R.; Fillmore, Mark T.

2016-01-01

Rationale Alcohol increases the tendency for risky driving in some individuals, but not others. Little is known about the factors underlying this individual difference. Studies find that those who underestimate their blood alcohol concentration (BAC) following a dose of alcohol tend to be more impulsive and report greater willingness to drive after drinking than those who estimate their BACs to be greater than their actual BAC. BAC underestimation could contribute to risky driving behavior following alcohol as such drivers might perceive little impairment in their driving ability and thus no need for caution. Objectives This study was designed to test the relationship between drivers’ BAC estimations following a dose of alcohol or a placebo and the degree of risky driving they displayed during a simulated driving test. Methods Forty adult drivers performed a simulated driving test and estimated their blood alcohol concentration after receiving a dose of alcohol (0.65 g/kg for men; 0.56 g/kg for women) or a placebo. . Results Alcohol increased risk taking and impaired driving skill. Those who estimated their BAC to be lower were the riskiest drivers following both alcohol and placebo. Conclusions The tendency to estimate lower BACs could support a series of high-risk decisions, regardless of one’s actual BAC. This could include the decision to drive after drinking. PMID:26861796

How predictive is breast arterial calcification of cardiovascular disease and risk factors when found at screening mammography?

PubMed

Kataoka, Masako; Warren, Ruth; Luben, Robert; Camus, Joanna; Denton, Erika; Sala, Elvis; Day, Nicholas; Khaw, Kay-Tee

2006-07-01

The purpose of this study was to examine the relationship between breast arterial calcification (BAC), commonly found on mammography, and cardiovascular disease and its risk factors. The study population, nested within the European Prospective Investigation of Cancer-Norfolk (EPIC-Norfolk) cohort study, consisted of 1,590 women older than 55 years, not taking hormone replacement therapy, and with available screening mammograms. Mammograms were coded by three radiologists for presence or absence of BAC. History of coronary heart disease (CHD), stroke, and diabetes and risk factors for cardiovascular disease (including smoking status, body mass index [BMI], blood pressure, diabetes, and glycosylated hemoglobin [HbA1c]) were independently measured from health examinations in the EPIC study. The prevalence of BAC was 16.0%. Women with BAC were significantly older than those without it. BAC was associated with prevalent CHD, but not stroke. The odds ratio of having CHD was 2.54 (95% confidence interval, 1.03-6.30). The sensitivity and specificity were 32.4% and 85.5%, respectively. Except for smoking, which showed an inverse association, there was no consistent significant association of BAC with cardiovascular disease risk factors including BMI, diabetes, HbA1c, or lipids. BAC found on mammograms was associated with prevalent CHD after adjustment for age, but with low sensitivity. BAC may provide additional information toward identifying cardiovascular disease risk among otherwise healthy women.

The 14/15 association as a paradigmatic example of tracing karyotype evolution in New World monkeys.

PubMed

Capozzi, Oronzo; Archidiacono, Nicoletta; Lorusso, Nicola; Stanyon, Roscoe; Rocchi, Mariano

2016-09-01

Fluorescence in situ hybridization (FISH), especially chromosome painting, has been extensively exploited in the phylogenetic reconstruction of primate evolution. Although chromosome painting is a key method to map translocations, it is not effective in detecting chromosome inversions, which may be up to four times more frequent than other chromosomal rearrangements. BAC-FISH instead can economically delineate marker order and reveal intrachromosomal rearrangements. However, up to now, BAC-FISH was rarely used to study the chromosomes of New World monkeys partly due to technical difficulties. In this paper, we used BAC-FISH to disentangle the complex evolutionary history of the ancestral 14/15 association in NWMs, beginning from the squirrel monkey (Saimiri boliviensis). To improve the hybridization efficiency of BAC-FISH in NWMs, we "translated" the human BACs into Callithrix jacchus (CJA) BACs, which yielded much higher hybridization efficiencies on other NWM species than human BACs. Our results disclosed 14 synteny blocks in squirrel monkeys, 7 more than with chromosome painting. We then applied a subset of CJA BACs on six other NWM species. The comparison of the hybridization pattern of these species contained phylogenetic information to discriminate evolutionary relationships. Notably Aotus was found to share an inversion with Callithrix, thus definitely assigning the genus Aotus to Cebidae. The present study can be seen as a paradigmatic approach to investigate the phylogenetics of NWMs by molecular cytogenetics.

Decay of Bacteroidales genetic markers in relation to traditional fecal indicators for water quality modeling of drinking water sources.

PubMed

Sokolova, Ekaterina; Aström, Johan; Pettersson, Thomas J R; Bergstedt, Olof; Hermansson, Malte

2012-01-17

The implementation of microbial fecal source tracking (MST) methods in drinking water management is limited by the lack of knowledge on the transport and decay of host-specific genetic markers in water sources. To address these limitations, the decay and transport of human (BacH) and ruminant (BacR) fecal Bacteroidales 16S rRNA genetic markers in a drinking water source (Lake Rådasjön in Sweden) were simulated using a microbiological model coupled to a three-dimensional hydrodynamic model. The microbiological model was calibrated using data from outdoor microcosm trials performed in March, August, and November 2010 to determine the decay of BacH and BacR markers in relation to traditional fecal indicators. The microcosm trials indicated that the persistence of BacH and BacR in the microcosms was not significantly different from the persistence of traditional fecal indicators. The modeling of BacH and BacR transport within the lake illustrated that the highest levels of genetic markers at the raw water intakes were associated with human fecal sources (on-site sewers and emergency sewer overflow). This novel modeling approach improves the interpretation of MST data, especially when fecal pollution from the same host group is released into the water source from different sites in the catchment.

Accelerated solvent extraction followed by on-line solid-phase extraction coupled to ion trap LC/MS/MS for analysis of benzalkonium chlorides in sediment samples

USGS Publications Warehouse

Ferrer, I.; Furlong, E.T.

2002-01-01

Benzalkonium chlorides (BACs) were successfully extracted from sediment samples using a new methodology based on accelerated solvent extraction (ASE) followed by an on-line cleanup step. The BACs were detected by liquid chromatography/ion trap mass spectrometry (LC/MS) or tandem mass spectrometry (MS/MS) using an electrospray interface operated in the positive ion mode. This methodology combines the high efficiency of extraction provided by a pressurized fluid and the high sensitivity offered by the ion trap MS/MS. The effects of solvent type and ASE operational variables, such as temperature and pressure, were evaluated. After optimization, a mixture of acetonitrile/water (6:4 or 7:3) was found to be most efficient for extracting BACs from the sediment samples. Extraction recoveries ranged from 95 to 105% for C12 and C14 homologues, respectively. Total method recoveries from fortified sediment samples, using a cleanup step followed by ASE, were 85% for C12BAC and 79% for C14-BAC. The methodology developed in this work provides detection limits in the subnanogram per gram range. Concentrations of BAC homologues ranged from 22 to 206 ??g/kg in sediment samples from different river sites downstream from wastewater treatment plants. The high affinity of BACs for soil suggests that BACs preferentially concentrate in sediment rather than in water.

New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits

PubMed Central

2011-01-01

Background Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18) to duodecaploid (12X = 108). Like in other large, repeat-rich plant genomes, this genomic complexity will hinder whole genome sequencing efforts. An extensive physical map providing enough information to resolve the homoeologous genomes would provide the necessary framework for accurate assembly of the switchgrass genome. Results A switchgrass BAC library constructed by partial digestion of nuclear DNA with EcoRI contains 147,456 clones covering the effective genome approximately 10 times based on a genome size of 3.2 Gigabases (~1.6 Gb effective). Restriction digestion and PFGE analysis of 234 randomly chosen BACs indicated that 95% of the clones contained inserts, ranging from 60 to 180 kb with an average of 120 kb. Comparative sequence analysis of two homoeologous genomic regions harboring orthologs of the rice OsBRI1 locus, a low-copy gene encoding a putative protein kinase and associated with biomass, revealed that orthologous clones from homoeologous chromosomes can be unambiguously distinguished from each other and correctly assembled to respective fingerprint contigs. Thus, the data obtained not only provide genomic resources for further analysis of switchgrass genome, but also improve efforts for an accurate genome sequencing strategy. Conclusions The construction of the first switchgrass BAC library and comparative analysis of homoeologous harboring OsBRI1 orthologs present a glimpse into the switchgrass genome structure and complexity. Data obtained demonstrate the feasibility of using HICF fingerprinting to resolve the homoeologous chromosomes of the two distinct genomes in switchgrass, providing a robust and accurate BAC-based physical platform for this species. The genomic resources and sequence data generated will lay the foundation for deciphering the switchgrass genome and lead the way for an accurate genome sequencing strategy. PMID:21767393

New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits.

PubMed

Saski, Christopher A; Li, Zhigang; Feltus, Frank A; Luo, Hong

2011-07-18

Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18) to duodecaploid (12X = 108). Like in other large, repeat-rich plant genomes, this genomic complexity will hinder whole genome sequencing efforts. An extensive physical map providing enough information to resolve the homoeologous genomes would provide the necessary framework for accurate assembly of the switchgrass genome. A switchgrass BAC library constructed by partial digestion of nuclear DNA with EcoRI contains 147,456 clones covering the effective genome approximately 10 times based on a genome size of 3.2 Gigabases (~1.6 Gb effective). Restriction digestion and PFGE analysis of 234 randomly chosen BACs indicated that 95% of the clones contained inserts, ranging from 60 to 180 kb with an average of 120 kb. Comparative sequence analysis of two homoeologous genomic regions harboring orthologs of the rice OsBRI1 locus, a low-copy gene encoding a putative protein kinase and associated with biomass, revealed that orthologous clones from homoeologous chromosomes can be unambiguously distinguished from each other and correctly assembled to respective fingerprint contigs. Thus, the data obtained not only provide genomic resources for further analysis of switchgrass genome, but also improve efforts for an accurate genome sequencing strategy. The construction of the first switchgrass BAC library and comparative analysis of homoeologous harboring OsBRI1 orthologs present a glimpse into the switchgrass genome structure and complexity. Data obtained demonstrate the feasibility of using HICF fingerprinting to resolve the homoeologous chromosomes of the two distinct genomes in switchgrass, providing a robust and accurate BAC-based physical platform for this species. The genomic resources and sequence data generated will lay the foundation for deciphering the switchgrass genome and lead the way for an accurate genome sequencing strategy.

Retrofitting BACs with G418 resistance, luciferase, and oriP and EBNA-1 – new vectors for in vitro and in vivo delivery

PubMed Central

Magin-Lachmann, Christine; Kotzamanis, George; D'Aiuto, Leonardo; Wagner, Ernst; Huxley, Clare

2003-01-01

Background Bacterial artificial chromosomes (BACs) have been used extensively for sequencing the human and mouse genomes and are thus readily available for most genes. The large size of BACs means that they can generally carry intact genes with all the long range controlling elements that drive full levels of tissue-specific expression. For gene expression studies and gene therapy applications it is useful to be able to retrofit the BACs with selectable genes such as G418 resistance, reporter genes such as luciferase, and oriP/EBNA-1 from Epstein Barr virus which allows long term episomal maintenance in mammalian cells. Results We describe a series of retrofitting plasmids and a protocol for in vivo loxP/Cre recombination. The vector pRetroNeo carries a G418 resistance cassette, pRetroNeoLuc carries G418 resistance and a luciferase expression cassette, pRetroNeoLucOE carries G418 resistance, luciferase and an oriP/EBNA-1 cassette and pRetroNeoOE carries G418 resistance and oriP/EBNA-1. These vectors can be efficiently retrofitted onto BACs without rearrangement of the BAC clone. The luciferase cassette is expressed efficiently from the retrofitting plasmids and from retrofitted BACs after transient transfection of B16F10 cells in tissue culture and after electroporation into muscles of BALB/c mice in vivo. We also show that a BAC carrying GFP, oriP and EBNA-1 can be transfected into B16F10 cells with Lipofectamine 2000 and can be rescued intact after 5 weeks. Conclusion The pRetro vectors allow efficient retrofitting of BACs with G418 resistance, luciferase and/or oriP/EBNA-1 using in vivo expression of Cre. The luciferase reporter gene is expressed after transient transfection of retrofitted BACs into cells in tissue culture and after electroporation into mouse muscle in vivo. OriP/EBNA-1 allows stable maintenance of a 150-kb BAC without rearrangement for at least 5 weeks. PMID:12609052

A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome

PubMed Central

2011-01-01

Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches. PMID:22142254

Effects of benzalkonium chloride on growth and survival of Chang conjunctival cells.

PubMed

De Saint Jean, M; Brignole, F; Bringuier, A F; Bauchet, A; Feldmann, G; Baudouin, C

1999-03-01

The aim of this study was to investigate the action of benzalkonium chloride (BAC), used as a preservative in most ophthalmic topical solutions, on epithelial conjunctival cells in vitro. A continuous human conjunctival cell line (Wong-Kilbourne derivative of Chang conjunctiva) was exposed to BAC solutions at various concentrations (0.1%-0.0001%) during a period of 10 minutes. Cells were examined before treatment and 3, 24, 48, and 72 hours later, after reexposure to normal cell culture conditions. Cell number and viability were assessed with crystal violet and 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl tetrazolium bromide colorimetric assays. The expression of the apoptotic marker Apo 2.7, nuclear antigen p53, membrane proteins Fas and Fas ligand, and DNA content was studied by flow cytometry. Morphologic aspects of cell nuclei were analyzed on slides with a nucleic acid-specific dye, 4',6'-diamidino-2-phenylindole dihydrochloride. Cytoskeleton was labeled with a monoclonal anti-pancytokeratin antibody. In addition, apoptosis was measured by DNA electrophoresis assays in agarose gel. Cell exposure to 0.1% and 0.05% BAC induced cell lysis immediately after treatment. All cells (100%) treated with 0.01% BAC died in a delayed manner within 24 hours, with most of the characteristics of apoptosis (chromatin condensation and DNA fragmentation, reduction in cell volume, expression of the apoptotic marker Apo 2.7, and apoptotic changes in DNA content). Aliquots of 0.005%, 0.001%, 0.0005%, and 0.0001% BAC induced growth arrest and apoptotic cell death in a dose-dependent manner between 24 and 72 hours after treatment. The expressions of Fas and p53 did not vary after BAC treatment. Fas ligand was always negative. These results suggest that BAC induces cell growth arrest and death at a concentration as low as 0.0001%. The mode of BAC-induced cell death is dose-dependent. Cells die by necrosis after BAC treatment at high concentrations and by apoptosis if low concentrations of BAC are applied. This new aspect of in vitro toxicity of BAC could in part explain some ocular surface disorders observed in patients undergoing long-term topical treatments with preservative-containing drugs.

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition.

PubMed

Si, Zengzhi; Du, Bing; Huo, Jinxi; He, Shaozhen; Liu, Qingchang; Zhai, Hong

2016-11-21

Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species. The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93-10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana. The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato.

Perceptions of alcohol-impaired driving and the blood alcohol concentration standard in the United States.

PubMed

Eby, David W; Molnar, Lisa J; Kostyniuk, Lidia P; St Louis, Renée M; Zanier, Nicole; Lepkowski, James M; Bergen, Gwen

2017-12-01

Although the number of alcohol-impaired driving (AID) fatalities has declined over the past several years, AID continues to be a serious public health problem. The purpose of this effort was to gain a better understanding of the U.S. driving population's perceptions and thoughts about the impacts of lowering the blood alcohol concentration (BAC) driving standard below.08% on AID, health, and other outcomes. A questionnaire was administered to a nationally representative sample of licensed drivers in the U.S. (n=1011) who were of age 21 or older on driving habits, alcohol consumption habits, drinking and driving habits, attitudes about drinking and driving, experiences with and opinions of drinking and driving laws, opinions about strategies to reduce drinking and driving, general concerns about traffic safety issues, and demographics. One-third of participants supported lowering the legal BAC standard, and participants rated a BAC standard of .05% to be moderately acceptable on average. 63.9% indicated that lowering 30 the BAC to .05% would have no effect on their decisions to drink and drive. Nearly 60% of respondents lacked accurate knowledge of their state's BAC standard. Public support for lowering the BAC standard was moderate and was partially tied to beliefs about the impacts of a change in the BAC standard. The results suggest that an opportunity for better educating the driving population about existing AID policy and the implications for lowering the BAC level on traffic injury prevention. The study results are useful for state traffic safety professionals and policy makers to have a better understanding of the public's perceptions of and thoughts about BAC standards. There is a clear need for more research into the effects of lowering the BAC standard on crashes, arrests, AID behavior, and alcohol-related behaviors. Copyright © 2017 National Safety Council and Elsevier Ltd. All rights reserved.

Organophilic treatments of bentonite increase the adsorption of aflatoxin B1 and protect stem cells against cellular damage.

PubMed

Nones, Janaína; Nones, Jader; Poli, Anicleto; Trentin, Andrea Gonçalves; Riella, Humberto Gracher; Kuhnen, Nivaldo Cabral

2016-09-01

Bentonite clays exhibit high adsorptive capacity for contaminants, including aflatoxin B1 (AFB1), a mycotoxin responsible for causing severe toxicity in several species including pigs, poultry and man. Organophilic treatments is known to increase the adsorption capacity of bentonites, and the primary aim of this study was to evaluate the ability of Brazilian bentonite and two organic salts - benzalkonium chloride (BAC) and cetyltrimethylammonium bromide (CTAB) to adsorb AFB1. For this end, 2(2) factorial designs were used in order to analyze if BAC or CTAB was able to increase AFB1 adsorption when submitted in different temperature and concentration. Both BAC and CTAB treatment (at 30°C and 2% of salt concentration) were found to increase the adsorption of AFB1 significantly compared with untreated bentonite. After organophilic bentonite treatments with BAC or CTAB, a vibration of CH stretch (2850 and 2920cm(-1)) were detected. A frequency of the SiO stretch (1020 and 1090cm(-1)) was changed by intercalation of organic cation. Furthermore, the interlayer spacing of bentonite increases to 1.23nm (d001 reflection at 2θ=7.16) and 1.22 (d001 reflection at 2θ=7.22) after the addition of BAC and CTAB, respectively. Another aim of the study was to observe the effects of these two bentonite salts in neural crest stem cell cultures. The two materials that were created by organophilic treatments were not found to be toxic to stem cells. Furthermore the results indicate that the two materials tested may protect the neural crest stem cells against damage caused by AFB1. Copyright © 2016 Elsevier B.V. All rights reserved.

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies.

PubMed

Tulpová, Zuzana; Luo, Ming-Cheng; Toegelová, Helena; Visendi, Paul; Hayashi, Satomi; Vojta, Petr; Paux, Etienne; Kilian, Andrzej; Abrouk, Michaël; Bartoš, Jan; Hajdúch, Marián; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2018-03-08

Bread wheat (Triticum aestivum L.) is a staple food for a significant part of the world's population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere. Copyright © 2018. Published by Elsevier B.V.

BAC and crash responsibility of injured older drivers : an analysis of Trauma Center data.

DOT National Transportation Integrated Search

2014-09-01

This study examined the distribution of blood alcohol concentrations (BACs) in injured drivers 65 and older and the relationship of older-driver BAC to driving record and crash responsibility. Researchers conducted a retrospective examination of 11 y...

The accuracy of evidential breath testers at low BACs

DOT National Transportation Integrated Search

1989-05-01

This Technical Note reports on the low blood alcohol concentration (BAC) laboratory testing of seven evidential breath testers widely used by law enforcement. The findings indicated that these devices are just as accurate at low BACs in the 0.020-0.0...

DiBAC4(3) hits a “sweet spot” for the activation of arterial large-conductance Ca2+-activated potassium channels independently of the β1-subunit

PubMed Central

Scornik, Fabiana S.; Bucciero, Ronald S.; Wu, Yuesheng; Selga, Elisabet; Bosch Calero, Cristina; Brugada, Ramon

2013-01-01

The voltage-sensitive dye bis-(1,3-dibutylbarbituric acid)trimethine oxonol [DiBAC4(3)] has been reported as a novel large-conductance Ca2+-activated K+ (BK) channel activator with selectivity for its β1- or β4-subunits. In arterial smooth muscle, BK channels are formed by a pore-forming α-subunit and a smooth muscle-abundant regulatory β1-subunit. This tissue specificity has driven extensive pharmacological research aimed at regulating arterial tone. Using animals with a disruption of the gene for the β1-subunit, we explored the effects of DiBAC4(3) in native channels from arterial smooth muscle. We tested the hypothesis that, in native BK channels, activation by DiBAC4(3) relies mostly on its α-subunit. We studied BK channels from wild-type and transgenic β1-knockout mice in excised patches. BK channels from brain arteries, with or without the β1-subunit, were similarly activated by DiBAC4(3). In addition, we found that saturating concentrations of DiBAC4(3) (∼30 μM) promote an unprecedented persistent activation of the channel that negatively shifts its voltage dependence by as much as −300 mV. This “sweet spot” for persistent activation is independent of Ca2+ and/or the β1–4-subunits and is fully achieved when DiBAC4(3) is applied to the intracellular side of the channel. Arterial BK channel response to DiBAC4(3) varies across species and/or vascular beds. DiBAC4(3) unique effects can reveal details of BK channel gating mechanisms and help in the rational design of BK channel activators. PMID:23542916

In Vitro Effects of Preserved and Unpreserved Anti-Allergic Drugs on Human Corneal Epithelial Cells

PubMed Central

Calvo, Patricia; Ropero, Inés; Pintor, Jesús

2014-01-01

Abstract Purpose: Treatment with topical eye drops for long-standing ocular diseases like allergy can induce detrimental side effects. The purpose of this study was to investigate in vitro cytotoxicity of commercially preserved and unpreserved anti-allergic eye drops on the viability and barrier function of monolayer and stratified human corneal-limbal epithelial cells. Methods: Cells were treated with unpreserved ketotifen solution, benzalkonium chloride (BAC)-containing anti-allergic drugs (ketotifen, olopatadine, levocabastine) as well as BAC alone. 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay was used to determine cell viability. Effects of compounds on barrier function were analyzed measuring transepithelial electrical resistance (TEER) to determine paracellular permeability and rose bengal assays to evaluate transcellular barrier formation. Results: The BAC-preserved anti-allergic formulations and BAC alone significantly reduced cell viability, monolayer cultures being more sensitive to damage by these solutions. Unpreserved ketotifen induced the least diminution in cell viability. The extent of decrease of cell viability was clearly dependent of BAC presence, but it was also affected by the different types of drugs when the concentration of BAC was low and the short time of exposure. Treatment with BAC-containing anti-allergic drugs and BAC alone resulted in increased paracellular permeability and loss of transcellular barrier function as indicated by TEER measurement and rose bengal assays. Conclusions: The presence of the preservative BAC in anti-allergic eye drop formulations contributes importantly to the cytotoxic effects induced by these compounds. Stratified cell cultures seem to be a more relevant model for toxicity evaluation induced on the ocular surface epithelia than monolayer cultures. PMID:25100331

Alterations in brain glucose utilization accompanying elevations in blood ethanol and acetate concentrations in the rat.

PubMed

Pawlosky, Robert J; Kashiwaya, Yoshihiro; Srivastava, Shireesh; King, Michael T; Crutchfield, Calvin; Volkow, Nora; Kunos, George; Li, Ting-Kai; Veech, Richard L

2010-02-01

Previous studies in humans have shown that alcohol consumption decreased the rate of brain glucose utilization. We investigated whether the major metabolite of ethanol, acetate, could account for this observation by providing an alternate to glucose as an energy substrate for brain and the metabolic consequences of that shift. Rats were infused with solutions of sodium acetate, ethanol, or saline containing (13)C-2-glucose as a tracer elevating the blood ethanol (BEC) and blood acetate (BAcC) concentrations. After an hour, blood was sampled and the brains of animals were removed by freeze blowing. Tissue samples were analyzed for the intermediates of glucose metabolism, Krebs' cycle, acyl-coenzyme A (CoA) compounds, and amino acids. Mean peak BEC and BAcC were approximately 25 and 0.8 mM, respectively, in ethanol-infused animals. Peak blood BAcC increased to 12 mM in acetate-infused animals. Both ethanol and acetate infused animals had a lower uptake of (13)C-glucose into the brain compared to controls and the concentration of brain (13)C-glucose-6-phosphate varied inversely with the BAcC. There were higher concentrations of brain malonyl-CoA and somewhat lower levels of free Mg(2+) in ethanol-treated animals compared to saline controls. In acetate-infused animals the concentrations of brain lactate, alpha-ketoglutarate, and fumarate were higher. Moreover, the free cytosolic [NAD(+)]/[NADH] was lower, the free mitochondrial [NAD(+)]/[NADH] and [CoQ]/[CoQH(2)] were oxidized and the DeltaG' of ATP lowered by acetate infusion from -61.4 kJ to -59.9 kJ/mol. Animals with elevated levels of blood ethanol or acetate had decreased (13)C-glucose uptake into the brain. In acetate-infused animals elevated BAcC were associated with a decrease in (13)C-glucose phosphorylation. The co-ordinate decrease in free cytosolic NAD, oxidation of mitochondrial NAD and Q couples and the decrease in DeltaG' of ATP was similar to administration of uncoupling agents indicating that the metabolism of acetate in brain caused the mitochondrial voltage dependent pore to form.

Alterations in Brain Glucose Utilization Accompanying Elevations in Blood Ethanol and Acetate Concentrations in the Rat

PubMed Central

Pawlosky, Robert J.; Kashiwaya, Yoshihiro; Srivastava, Shireesh; King, Michael T.; Crutchfield, Calvin; Volkow, Nora; Kunos, George; Li, Ting-Kai; Veech, Richard L.

2010-01-01

Background Previous studies in humans have shown that alcohol consumption decreased the rate of brain glucose utilization. We investigated whether the major metabolite of ethanol, acetate, could account for this observation by providing an alternate to glucose as an energy substrate for brain and the metabolic consequences of that shift. Methods Rats were infused with solutions of sodium acetate, ethanol, or saline containing 13C-2-glucose as a tracer elevating the blood ethanol (BEC) and blood acetate (BAcC) concentrations. After an hour, blood was sampled and the brains of animals were removed by freeze blowing. Tissue samples were analyzed for the intermediates of glucose metabolism, Krebs’ cycle, acyl-coenzyme A (CoA) compounds, and amino acids. Results Mean peak BEC and BAcC were approximately 25 and 0.8 mM, respectively, in ethanol-infused animals. Peak blood BAcC increased to 12 mM in acetate-infused animals. Both ethanol and acetate infused animals had a lower uptake of 13C-glucose into the brain compared to controls and the concentration of brain 13C-glucose-6-phosphate varied inversely with the BAcC. There were higher concentrations of brain malonyl-CoA and somewhat lower levels of free Mg2+ in ethanol-treated animals compared to saline controls. In acetate-infused animals the concentrations of brain lactate, α-ketoglutarate, and fumarate were higher. Moreover, the free cytosolic [NAD+]/[NADH] was lower, the free mitochondrial [NAD+]/[NADH] and [CoQ]/[CoQH2] were oxidized and the ΔG′ of ATP lowered by acetate infusion from −61.4 kJ to −59.9 kJ/mol. Conclusions Animals with elevated levels of blood ethanol or acetate had decreased 13C-glucose uptake into the brain. In acetate-infused animals elevated BAcC were associated with a decrease in 13C-glucose phosphorylation. The co-ordinate decrease in free cytosolic NAD, oxidation of mitochondrial NAD and Q couples and the decrease in ΔG′ of ATP was similar to administration of uncoupling agents indicating that the metabolism of acetate in brain caused the mitochondrial voltage dependent pore to form. PMID:19951290

Construction of BAC Libraries from Flow-Sorted Chromosomes.

PubMed

Šafář, Jan; Šimková, Hana; Doležel, Jaroslav

2016-01-01

Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes.

Angiopoietin-1-expressing adipose stem cells genetically modified with baculovirus nanocomplex: investigation in rat heart with acute infarction.

PubMed

Paul, Arghya; Nayan, Madhur; Khan, Afshan Afsar; Shum-Tim, Dominique; Prakash, Satya

2012-01-01

The objective of this study was to develop angiopoietin-1 (Ang1)-expressing genetically modified human adipose tissue derived stem cells (hASCs) for myocardial therapy. For this, an efficient gene delivery system using recombinant baculovirus complexed with cell penetrating transactivating transcriptional activator TAT peptide/deoxyribonucleic acid nanoparticles (Bac-NP), through ionic interactions, was used. It was hypothesized that the hybrid Bac- NP(Ang1) system can efficiently transduce hASCs and induces favorable therapeutic effects when transplanted in vivo. To evaluate this hypothesis, a rat model with acute myocardial infarction and intramyocardially transplanted Ang1-expressing hASCs (hASC-Ang1), genetically modified by Bac-NP(Ang1), was used. Ang1 is a crucial pro-angiogenic factor for vascular maturation and neovasculogenesis. The released hAng1 from hASC-Ang1 demonstrated profound mitotic and anti-apoptotic activities on endothelial cells and cardiomyocytes. The transplanted hASC-Ang1 group showed higher cell retention compared to hASC and control groups. A significant increase in capillary density and reduction in infarct sizes were noted in the infarcted hearts with hASC-Ang1 treatment compared to infarcted hearts treated with hASC or the untreated group. Furthermore, the hASC-Ang1 group showed significantly higher cardiac performance in echocardiography (ejection fraction 46.28% ± 6.3%, P < 0.001 versus control, n = 8) than the hASC group (36.35% ± 5.7%, P < 0.01, n = 8), 28 days post-infarction. The study identified Bac-NP complex as an advanced gene delivery vehicle for stem cells and demonstrated its potential to treat ischemic heart disease with high therapeutic index for combined stem cell-gene therapy strategy.

Chemosaturation with Percutaneous Hepatic Perfusion for Unresectable Isolated Hepatic Metastases from Sarcoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deneve, Jeremiah L., E-mail: Jeremiah.Deneve@Moffitt.org; Choi, Junsung; Gonzalez, Ricardo J.

Purpose: Treatment of patients with unresectable liver metastases is challenging. Regional therapies to the liver have been developed that maximize treatment of the localized disease process without systemic toxic adverse effects. We discuss the procedural aspects of liver chemosaturation with percutaneous hepatic perfusion (CS-PHP). Methods: We present as an illustration of this technique a case report of the treatment of unresectable metastatic leiomyosarcoma of the liver. Results: A randomized phase III trial for unresectable liver metastases from melanoma was recently completed comparing CS-PHP with melphalan vs. best alternative care (BAC). When compared with BAC, CS-PHP was associated with a significantmore » improvement in hepatic progression-free survival (8.0 months CS-PHP vs. 1.6 months BAC, p < 0.0001) and overall progression-free survival (6.7 months CS-PHP vs. 1.6 months BAC, p < 0.0001), respectively. On the basis of these results, and given our experience as one of the treating institutions for this phase III trial, we appealed for compassionate use of CS-PHP in a patient with isolated bilobar unresectable hepatic metastases from leiomyosarcoma. Four target lesions were identified and monitored to assess treatment response. A total of 4 CS-PHP procedures were performed, with a 25 % reduction in size of the largest lesion observed and 16 month hepatic progression-free survival. Toxicity was mild (neutropenia) and manageable on an outpatient basis. Conclusion: CS-PHP offers several advantages for unresectable hepatic sarcoma metastases. CS-PHP is minimally invasive and repeatable, and it has a predictable and manageable systemic toxicity profile. For appropriately selected patients, CS-PHP can delay tumor progression and could potentially improve survival.« less

Evaluation of enhanced sanctions for higher BACs : summary of states' laws

DOT National Transportation Integrated Search

2001-03-01

Twenty-nine states have a stature, regulation, or rule that provides for additional or more severe sanctions for driving under the influence (DUI) offenders with a "high" BAC. States vary in terms of the high-BAC threshold, which ranges from .15 to ....

BAC Modification through Serial or Simultaneous Use of CRE/Lox Technology

PubMed Central

Parrish, Mark; Unruh, Jay; Krumlauf, Robb

2011-01-01

Bacterial Artificial Chromosomes (BACs) are vital tools in mouse genomic analyses because of their ability to propagate large inserts. The size of these constructs, however, prevents the use of conventional molecular biology techniques for modification and manipulation. Techniques such as recombineering and Cre/Lox methodologies have thus become heavily relied upon for such purposes. In this work, we investigate the applicability of Lox variant sites for serial and/or simultaneous manipulations of BACs. We show that Lox spacer mutants are very specific, and inverted repeat variants reduce Lox reaction rates through reducing the affinity of Cre for the site, while retaining some functionality. Employing these methods, we produced serial modifications encompassing four independent changes which generated a mouse HoxB BAC with fluorescent reporter proteins inserted into four adjacent Hox genes. We also generated specific, simultaneous deletions using combinations of spacer variants and inverted repeat variants. These techniques will facilitate BAC manipulations and open a new repertoire of methods for BAC and genome manipulation. PMID:21197414

Dynamic behavior of pump light radiation induced photo-bleaching effect on BAC-Si in bismuth/erbium co-doped optical fibers

NASA Astrophysics Data System (ADS)

Ding, Mingjie; Luo, Yanhua; Wen, Jianxiang; Peng, Gang-Ding

2018-02-01

Ultra-wide emission in bismuth doped optical fiber has been extremely studied for the development of the laser and amplifier working at near infrared band. In our homemade bismuth/erbium co-doped optical fiber, bismuth active center associated with silica (BAC-Si) has been found that when pumping at its resonant wavelength at 830 nm the NIR emission could be partially bleached. In addition, a self-recovery process has been observed at room temperature. However, the exact mechanism is still unclear. In this work, we have investigated the photo-bleaching effect on the BAC-Si via the pump power, pump wavelength and temperature dependence. Based on analyzing the result using stretched exponential function, it shows that the bleaching effect on BAC-Si has a strong link with the excitation process of Bi ion in BAC-Si. A potential energy curve model is used to illustrate the BAC-Si photo-bleaching process.

A comparison of breath- and blood-alcohol test results from real-life policing situations: a one-year study of data from the Central Hessian police district in Germany.

PubMed

Roiu, Immanuel; Birngruber, Christoph G; Spencer, Victoria C; Wollersen, Heike; Dettmeyer, Reinhard; Verhoff, Marcel A

2013-10-10

So far, studies investigating the comparability of breath alcohol concentration (BrAC) with blood alcohol concentration (BAC) have focused on the accuracy of BrAC testing instruments. The presented study, conducted with cases from the district of the Middle Hessian Police Headquarters, is to the best of our knowledge the first to compare both methods under real-life conditions in normal policing situations. For a 1-year period, alcohol-impaired drunk-driving suspects, who were by criminal procedure required to give a blood sample, were offered a voluntary, additional BrAC test with a "Dräger Alcotest 7110 Evidential". The BrAC test was to be administered as soon as possible after the suspect had been apprehended, without, however, delaying the collection of the blood sample. Ninety-two cases could be included in our study. In 30 cases, a blood sample was not taken; in 11 cases, a BrAC test could not be performed. In the remaining 51 cases, we found the following pairings of BrAC and BAC results: BrAC≥0.55 mg/l and BAC≥1.1‰ (n=39); 0.25 mg/l≤BrAC<0.55 mg/l and 0.5‰≤BAC<1.1‰ (n=5); BrAC≥0.55 mg/l and BAC<1.1‰ (n=4); BrAC<0.55 mg/l and BAC≥1.1‰ (n=3). The mean value for the conversion factor, Q, was 2.12‰l/mg. In accord with numerous other studies, our study results would suggest a value of 2.1‰ l/mg to German legislature as a new statutory value for Q. In borderline cases, of which there were already 7 in our study with 51 cases, suspects could benefit both from a BrAC test or a BAC test, with the benefit lastly depending more on early testing time than on the test method used. Our results support the call for the earliest possible measurement of alcohol concentration values after a drunk driving offense was committed. In some situations, this can probably only be accomplished with BrAC testing. A supplementary blood sample and BAC testing could compensate for the known weaknesses of BrAC testing. Thus, the complementary use of both methods might be a viable option. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Leakage of soluble microbial products from biological activated carbon filtration in drinking water treatment plants and its influence on health risks.

PubMed

Hong, Shen; Xian-Chun, Tang; Nan-Xiang, Wu; Hong-Bin, Chen

2018-07-01

The application of ozone-biological activated carbon (O 3 -BAC) as an advanced treatment method in drinking water treatment plants (DWTPs) can help to remove organic micropollutants and further decrease the dissolved organic carbon (DOC) level in finished water. With the increase attention to microbial safety of drinking water, a pre-positioned O 3 -BAC followed by a sand filter has been implanted into DWTP located in Shanghai, China to increase the biostability of effluents. The results showed that BAC had high removal efficiencies of UV 254 , DOC and disinfection by-product formation potential (DBPFP). The removal efficiencies between pre- and post-positioned BAC filtrations were similar. Based on the analyses of fluorescence excitation-emission matrix spectrophotometry (FEEM), the generation and leakage of soluble microbial products (SMPs) were found in both two BAC filtrations on account of the increased fluorescence intensities and fluorescence regional integration (FRI) distribution of protein-like organics, as well as the enhanced biological index (BIX). The leakage of SMPs produced by metabolism of microbes during BAC process resulted in increased DBPFP yield and carcinogenic factor per unit of DOC (CF/DOC). Although BAC filtration reduced the DBPFP and CF, there still was high health risk of effluents for the production of SMPs. Therefore, the health risks for SMPs generated by BAC filtration in drinking water advanced treatment process should be addressed, especially with that at high temperature. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Novel Ideal Radionuclide Imaging System for Non-invasively Cell Monitoring built on Baculovirus Backbone by Introducing Sleeping Beauty Transposon

PubMed Central

Lv, Jing; Pan, Yu; Ju, Huijun; Zhou, Jinxin; Cheng, Dengfeng; Shi, Hongcheng; Zhang, Yifan

2017-01-01

Sleeping Beauty (SB) transposon is an attractive tool in stable transgene integration both in vitro and in vivo; and we introduced SB transposon into recombinant sodium-iodide symporter baculovirus system (Bac-NIS system) to facilitate long-term expression of recombinant sodium-iodide symporter. In our study, two hybrid baculovirus systems (Bac-eGFP-SB-NeoR and Bac-NIS-SB-NeoR) were successfully constructed and used to infect U87 glioma cells. After G418 selection screening, the Bac-eGFP-SB-NeoR-U87 cells remained eGFP positive, at the 18th and 196th day post transfection (96.03 ± 0.21% and 97.43 ± 0.81%), while eGFP positive population declined significantly at 18 days in cells transfected with unmodified baculovirus construct. NIS gene expression by Bac-NIS-SB-NeoR-U87 cells was also maintained for 28 weeks as determined by radioiodine uptake assay, reverse transcription-polymerase chain reaction (RT-PCR) and Western Blot (WB) assay. When transplanted in mice, Bac-NIS-SB-NeoR-U87 cells also expressed NIS gene stably as monitored by SPECT imaging for 43 days until the tumor-bearing mice were sacrificed. Herein, we showed that incorporation of SB in Bac-NIS system (hybrid Bac-NIS-SB-NeoR) can achieve a long-term transgene expression and can improve radionuclide imaging in cell tracking and monitoring in vivo. PMID:28262785

Characterizing a novel strain of Bacillus amyloliquefaciens BAC03 for potential biological control application

USDA-ARS?s Scientific Manuscript database

Aims: Identify and characterize a bacterial strain from suppressive soil, BAC03, evaluate its antimicrobial activity against Streptomyces scabies and other microorganisms, and characterize an antimicrobial substance produced by this strain. Methods and Results: Bacterial strain BAC03 (isolated from ...

Attenuation of cytotoxicity induced by tBHP in H9C2 cells by Bacopa monniera and Bacoside A.

PubMed

T, Mohan Manu; Anand, T; Khanum, Farhath

2018-06-01

Cardiovascular diseases are one of the major global health issues leading to morbidity and mortality across the world. In the present study Bacopa monniera and its major bioactive component, Bacoside A (Bac-A) was used to evaluate its cytoprotective property in H9C2 cardiomyocytes against tBHP (150 μM) induced ROS-mediated oxidative stress and apoptosis. Our results implicate that pre-treatment with hydroalcoholic extract of Bacopa monniera (BME) and Bac-A (125 μg/ml and 6 μg/ml respectively) significantly restored oxidative stress by scavenging the free radicals and also elevated phase II antioxidant defensive enzymes such as (SOD, CAT, GR, GPx and GSH). Membrane integrity was estimated by MMP and LDH assays and found 89 and 72% of the protective effect. Further immunoblotting studies confirmed anti-apoptotic effects by regulating protein expression like Bcl2 was up-regulated to 99 and 85% and Bax was down-regulated to 122 and 181%, iNOS by 154.38 and 183.45% compared to tBHP (277.48%) by BME and Bac-A. BME and Bac-A exerts cytoprotective efficacy by attenuation of ROS generated through oxidative stress by an increase in the concentration of antioxidant enzymes and sustain membrane integrity which leads to restoring the damage caused by tBHP. Copyright © 2018 Elsevier B.V. All rights reserved.

Self-assembly of bacitracin-gold nanoparticles and their toxicity analysis.

PubMed

Li, Xiaoling; Wang, Zi; Li, Yanji; Bian, Kexin; Yin, Tian; Gao, Dawei

2018-01-01

As the widely use of gold nanoparticles (AuNPs) in drug delivery, the precise control on the size and morphology of the AuNPs is urgently required. In this scenario, traditional synthesis methods cannot meet current requirement because of their inherent defects. We have depicted here a novel method for fabricating monodispersed large size gold nanoparticles, based on the self-assembly of bacitracin. The AuNPs could be facilely, low-cost, and green synthesized with repeatability and controllability in this method. The Bac gold nanoparticles (Bac-AuNPs), composed by bacitracin core and gold shell, exhibited a spherical morphology in TEM and a face-centered cubic crystal structure in X-Ray diffraction and selected area electron diffraction. The mean diameter of the Bac-AuNPs was 89nm. The nanoparticles were mono-dispersed and the zeta potential of the nanoparticles was 4.1±0.64mV. Notably, in cell viability assay, the Bac-AuNPs showed less toxicity to HepG2 cells and HEK293 cells compared to small size AuNPs. Collectively, the size, rheological characteristic and the biocompatibility supported the use of the gold nanoparticles as intracellular delivery vehicles for drug delivery, especially for tumor therapy. And this study could provide a maneuverable, controllable and green strategy for the synthesis of AuNPs, which would be applied in disease diagnosis and therapy with biosafety. Copyright © 2017. Published by Elsevier B.V.

The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution.

PubMed

Cao, Hieu Xuan; Vu, Giang Thi Ha; Wang, Wenqin; Appenroth, Klaus J; Messing, Joachim; Schubert, Ingo

2016-01-01

Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species. © 2015 IPK Gatersleben. New Phytologist © 2015 New Phytologist Trust.

Effect of ozone on the performance of a hybrid ceramic membrane-biological activated carbon process.

PubMed

Guo, Jianning; Hu, Jiangyong; Tao, Yi; Zhu, Jia; Zhang, Xihui

2014-04-01

Two hybrid processes including ozonation-ceramic membrane-biological activated carbon (BAC) (Process A) and ceramic membrane-BAC (Process B) were compared to treat polluted raw water. The performance of hybrid processes was evaluated with the removal efficiencies of turbidity, ammonia and organic matter. The results indicated that more than 99% of particle count was removed by both hybrid processes and ozonation had no significant effect on its removal. BAC filtration greatly improved the removal of ammonia. Increasing the dissolved oxygen to 30.0 mg/L could lead to a removal of ammonia with concentrations as high as 7.80 mg/L and 8.69 mg/L for Processes A and B, respectively. The average removal efficiencies of total organic carbon and ultraviolet absorbance at 254 nm (UV254, a parameter indicating organic matter with aromatic structure) were 49% and 52% for Process A, 51% and 48% for Process B, respectively. Some organic matter was oxidized by ozone and this resulted in reduced membrane fouling and increased membrane flux by 25%-30%. However, pre-ozonation altered the components of the raw water and affected the microorganisms in the BAC, which may impact the removals of organic matter and nitrite negatively. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Transformation of Escherichia coli with large DNA molecules by electroporation.

PubMed Central

Sheng, Y; Mancino, V; Birren, B

1995-01-01

We have examined bacterial electroporation with a specific interest in the transformation of large DNA, i.e. molecules > 100 kb. We have used DNA from bacterial artificial chromosomes (BACs) ranging from 7 to 240 kb, as well as BAC ligation mixes containing a range o different sized molecules. The efficiency of electroporation with large DNA is strongly dependent on the strain of Escherichia coli used; strains which offer comparable efficiencies for 7 kb molecules differ in their uptake of 240 kb DNA by as much as 30-fold. Even with a host strain that transforms relatively well with large DNA, transformation efficiency drops dramatically with increasing size of the DNA. Molecules of 240 kb transform approximately 30-fold less well, on a molar basis, than molecules of 80 kb. Maximum transformation of large DNA occurs with different voltage gradients and with different time constants than are optimal for smaller DNA. This provides the opportunity to increase the yield of transformants which have taken up large DNA relative to the number incorporating smaller molecules. We have demonstrated that conditions may be selected which increase the average size of BAC clones generated by electroporation and compare the overall efficiency of each of the conditions tested. Images PMID:7596828

Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome

PubMed Central

Ríos, Gabino; Naranjo, Miguel A; Iglesias, Domingo J; Ruiz-Rivero, Omar; Geraud, Marion; Usach, Antonio; Talón, Manuel

2008-01-01

Background Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background. Results Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues. Conclusion In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with Populus trichocarpa than with the phylogenetically closer Arabidopsis thaliana. This work corroborates the potential of Citrus genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement. PMID:18691431

Evaluation of the effects of North Carolina's 0.8% BAC laws

DOT National Transportation Integrated Search

1998-11-12

This report describes a study of the effects of the North Carolina 0.08% blood alcohol concentration (BAC) limit on alcohol-related crashes. On October 1, 1993 the per se illegal BAC limit for drivers was reduced from 0.10% to 0.08%. To determine wha...

A non-autonomous insect piggyBac trasposable element is mobile in tobacco

USDA-ARS?s Scientific Manuscript database

The piggyBac transposable element, originally isolated from a virus in an insect cell line, is a valuable molecular tool for transgenesis and mutagenesis of invertebrates. For heterologous transgenesis in a variety of mammals, transfer of the piggyBac transposable element from an ectopic plasmid onl...

Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project.

PubMed

Park, Tae-Ho; Park, Beom-Seok; Kim, Jin-A; Hong, Joon Ki; Jin, Mina; Seol, Young-Joo; Mun, Jeong-Hwan

2011-01-01

As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome (BAC) by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa. Copyright © 2011. Published by Elsevier Ltd.

Impact of lowering the legal blood alcohol concentration limit to 0.03 on male, female and teenage drivers involved alcohol-related crashes in Japan.

PubMed

Desapriya, E; Shimizu, S; Pike, I; Subzwari, S; Scime, G

2007-09-01

In June of 2002, a revision to part of the Road Traffic Act drastically increased the penalties for drinking and driving offences in Japan. Most notably, the legal blood alcohol concentration (BAC) limit for driving was lowered from 0.05 mg/ml to 0.03 mg/ml. The rationale for the new lower BAC limit was predicated on the assumption that drinking drivers will comply with the new, lower limit by reducing the amount of alcohol they consume prior to driving, thereby lowering their risk of crash involvement. This, in turn, would lead to fewer alcohol-related crashes. A key limitation of previous lower BAC evaluation research in determining the effectiveness of lower legal BAC limit policies is the assumption of population homogeneity in responding to the laws. The present analysis is unique in this perspective and focuses on the evaluation of the impact of BAC limit reduction on different segments of the population. The chief objective of this research is to quantify the extent to which lowering the legal limit of BAC has reduced male, female and teenager involvement in motor vehicle crashes in Japan since 2002. Most notably, the introduction of reduced BAC limit legislation resulted in a statistically significant decrease in the number of alcohol-impaired drivers on the road in Japan, indicating responsiveness to the legal change among adults and teenagers. In addition, this preliminary assessment appears to indicate that the implementation of 0.03 BAC laws and other associated activities are associated with statistically significant reductions in alcohol-involved motor vehicle crashes. In comparison, the rates of total crashes showed no statistically significant decline nor increase in the period following the introduction of the BAC law, indicating that the lower BAC limit only had an effect on alcohol-related crashes in Japan. The evidence suggests that the lower BAC legal limit and perceived risk of detection are the two most important factors resulting in a sustained change in drinking and driving behaviour in Japan. It is recommended that future research and resources in other countries be focused on these factors as determinants to reduced alcohol-related crashes.

International policies on alcohol impaired driving: are legal blood alcohol concentration (BAC) limits in motorized countries compatible with the scientific evidence?

PubMed

Desapriya, E B R; Iwase, Nobutada; Brussoni, Mariana; Shimizu, Shinji; Belayneh, Taye N

2003-04-01

Borkenstein et al. (1974) study indicated that drivers with BACs of 0.05 to 0.09 per cent were twice as likely to crash as drivers with a zero BAC. Drivers with BACs from 0.10 to 0.14 per cent were ten times as likely to have a fatal crash in 1964. There have been numerous efforts during the history of motorized countries to control the consumption of alcohol and the problems associated with it through legislative mandate, it was not until the 1970s that acceptance of legal BAC (Blood Alcohol Concentration) limits laws became widespread. In particular, as more and more people drive automobiles, the number of traffic accidents involving drunken drivers has soared, and many of these are known to be related to the consumption of alcohol. Thus, legislators find themselves under increasing pressure to find a reasonable and fair solution to the question of alcohol impaired driving, as the scientific evidence about alcohol consumption level and psycho motor functions impairment came to clear. A landmark event in the development of policies regarding impaired driving was the establishment of the fact that consumption of alcohol does, in fact, increase the probability of traffic crashes. Legal limit laws specify a maximum permissible BAC limit for drivers. Currently, a BAC laws range from zero tolerance and 0.02 to 0.10% constitutes prima facie evidence in most countries for 'Driving under Influence of Alcohol.' This latter standard is too permissive, as driving skills deteriorate and crash involvement risk increases beginning at 0.02%. There are consequences attached to setting a BAC limit so high that a 72 kg man can drink five bottles of beer and still be under legal limit. In this sense high legal BAC limit may influence people to make bad estimates of their relative risk of injury or death while driving. Provided there is adequate political will, millions of lives could be saved in the coming years. This review is an attempt to examine in detail the available information about legal BAC limit laws, and issue of considerable interest to both policy makers and the public.

Driving decisions when leaving electronic music dance events: driver, passenger, and group effects.

PubMed

Johnson, Mark B; Voas, Robert B; Miller, Brenda A

2012-01-01

The goal of this article was to identify characteristics of drivers and passengers that predicted peer groups whose drivers exit dance clubs with alcohol levels indicative of impairment (blood alcohol content [BAC] ≥ 0.05 g/dL). We used the portal survey methodology to randomly sample groups of electronic music dance event (EMDE) patrons as they entered and exited a club. From May through November 2010, data were collected from 38 EMDEs hosted by 8 clubs in the San Francisco Bay area. Data included in these analyses are results from breath samples for measuring BAC and self-report data on demographics, recent drinking history drinking, drinking intentions, travel to and from the clubs, and the familiarity/experience with other group members. These data were collected from a subset of 175 drivers and 272 passengers. Although drivers drank less than passengers, one driver in 5 groups had a BAC indicative of elevated crash risk (BAC ≥ 0.05 g/dL). Groups of drivers and/or passengers with a recent history of binge drinking were more likely to have drivers with BACs ≥ 0.05 g/dL. One unanticipated finding was that drivers who knew more group members relatively well were more likely to exit the club with a BAC ≥ 0.05 g/dL. Additionally, we found that groups with all female passengers were at greater risk for having a driver whose BAC was ≥ 0.05 g/dL. Some group characteristics predicted drivers who exit clubs with BACs ≥ 0.05 g/dL. One intervention strategy to promote safety might be to encourage group members to reconsider who is sober enough to drive away from the club; for some groups, a change of drivers would be a safer choice, because a passenger may have a relatively safe BAC. Groups of females appear to have a particularly elevated risk of having a driver whose BAC exceeds 0.05 g/dL, and new intervention efforts should be particularly directed to these at-risk groups.

Control Characteristics of Alcohol-Impaired Operators

NASA Technical Reports Server (NTRS)

Jex, Henry R.; McRuer, Duane T.; Allen, R. Wade; Klein, Richard H.

1974-01-01

Although the operation of vehicles like airplanes, cars, and bicycles involves a complex array of perceptual, decision and control activities, most accident statistics clearly show that intoxicated operators are a dominant cause of accidents, and not the difficulty of the task itself. This paper summarizes some recent research on the nature of the impairment of operator control under blood alcohol concentrations (BAC) up to above 0.16 percent. Alcohol toxicity is shown to be quite specific with respect to visual-motor functions involved in control of a vehicle, and experiments with a generalized workload task and special driving simulator show how these are reflected in terms of changes in operator control parameters such as response latency, gains, stability margins, and coherency.

Toward a Molecular Cytogenetic Map for Cultivated Sunflower (Helianthus annuus L.) by Landed BAC/BIBAC Clones

PubMed Central

Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

2013-01-01

Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (∼100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC- fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)−derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources. PMID:23316437

The NASOROSSO (Rednose) Project: An Italian Study on Alcohol Consumption in Recreational Places

PubMed Central

Pacifici, Roberta; Pierantozzi, Andrea; Di Giovannandrea, Rita; Palmi, Ilaria; Mastrobattista, Luisa; Mortali, Claudia; Pichini, Simona

2013-01-01

The Nasorosso project of the Italian Youth Department and the National Institute of Health, aimed to raise awareness about drinking and driving under the influence of alcohol among club goers with a series of initiatives. Within the framework of the project, blood alcohol concentration (BAC) was measured on 106,406 individuals before and after clubbing in 66 different recreational sites from 11 Italian provinces, over 16 months. Participating individuals were interviewed regarding sociodemographic and environmental characteristics and alcohol intoxicated people were offered to be taken home. The BAC median at the club entry was 0.26 g/L with 65.3% subjects showing a BAC value under the driving legal limit of 0.5g/L. At the exit from clubs, BAC median value rose to 0.44 g/L and subjects with BAC value under the legal limit decreased to 54.9%. Being male, aged between 18 and 34 years with a diploma, being a drinker and entering the disco with a BAC already beyond the legal limit predicted a BAC value beyond 0.5 g/L at exit from the recreational place. Conversely, being a driver, being a student and exiting from the disco before 4 a.m. reduced the probability of having a BAC higher than 0.5 g/L at the end of the night. Health policies to prevent harmful use of alcohol in young people should continue to offer targeted information/ prevention; in order to steadily increase the awareness of the dangers and the damages of excessive use of alcohol. PMID:23615454

Extension of the simulated drinking game procedure to multiple drinking games.

PubMed

Cameron, Jennifer M; Leon, Matthew R; Correia, Christopher J

2011-08-01

The present study extended the Simulated Drinking Game Procedure (SDGP) to obtain information about different types of drinking games. Phase I participants (N = 545) completed online screening questionnaires assessing substance use and drinking game participation. Participants who met the selection criteria for Phase II (N = 92) participated in laboratory sessions that consisted of three different periods of drinking game play. Sixty-two percent (N = 57) of the sample was female. Data from these sessions was used to estimate the peak Blood Alcohol Concentration (BAC) a participant would achieve if they consumed alcohol while participating in the SDGP. Total consumption and estimated BAC varied as a function of game type. The total consumption and estimated BAC obtained while playing Beer Pong and Memory varied significantly as a function of group. Total ounces consumed while playing Three Man varied significantly as a function of group; however, the variation in estimated BAC obtained while playing Three Man was not significant. Results indicated that estimated BACs were higher for female participants across game type. Previous experience playing the three drinking games had no impact on total drink consumption or estimated BAC obtained while participating in the SDGP. The present study demonstrated that the SDGP can be used to generate estimates of how much alcohol is consumed and the associated obtained BAC during multiple types of drinking games. In order to fully examine whether previous experience factors in to overall alcohol consumption and BAC, future research should extend the SDGP to incorporate laboratory administration of alcohol during drinking game participation. (c) 2011 APA, all rights reserved.

Use of BAC clones as standardized reagents for Marek’s disease virus research

USDA-ARS?s Scientific Manuscript database

The cloning of the Marek’s disease virus (MDV) genome as an infectious bacterial artificial chromosome (BAC) clone have led to major advances through our ability to study individual gene function by making precise insertions and deletions in the viral genome. We believe that MDV BAC clones will repl...

State Blood Alcohol Concentration (BAC) Testing and Reporting for Drivers Involved in Fatal Crashes : Current Practices, Results, and Strategies, 1997-2009

DOT National Transportation Integrated Search

2012-08-01

This report documents current State blood alcohol concentration (BAC) testing and reporting practices and results for drivers involved in fatal crashes. It summarizes known BAC results by State for the years 1997 to 2009 for both fatally injured and ...

BAC to degeneration bacterial artificial chromosome (BAC)-mediated transgenesis for modeling basal ganglia neurodegenerative disorders.

PubMed

Lu, Xiao-Hong

2009-01-01

Basal ganglia neurodegenerative disorders, such as Parkinson's disease (PD) and Huntington's disease (HD), are characterized by not only spectrum of motor deficits, ranging form hypokinesia to hyperkinesia, but also emotional, cognitive, and psychiatric manifestations. The symptoms and pathogenic mechanism of these disorders should be viewed as dysfunctions of specific cortico-subcortical neurocircuits. Transgenic approaches using large genomic inserts, such as bacterial artificial chromosome (BAC)-mediated transgenesis, due to its capacity to propagate large-size genomic DNA and faithful production of endogenous-like gene expression pattern/lever, have provided an ideal basis for the generation of transgenic mice as model for basal ganglia neurodegenerative disorders, as well as the functional and structural analysis of neurocircuits. In this chapter, the basic concepts and practical approaches about application of BAC transgenic system are introduced. Existent major BAC transgenic mouse models for PD and HD are evaluated according to their construct, face, and predicative validity. Finally, considerations, possible solutions, and future perspectives of using BAC transgenic approach to study basal ganglia neurodegenerative disorders are discussed.

Purification and partial characterization of a novel antibacterial agent (Bac1829) Produced by Staphylococcus aureus KSI1829.

PubMed Central

Crupper, S S; Iandolo, J J

1996-01-01

A novel antimicrobial agent from Staphylococcus aureus KSI1829, designated Bac1829, was purified by sequential steps of ammonium sulfate precipitation, Sephadex G-50 gel filtration chromatography, and hydrophobic interaction chromatography. Purified Bac1829 has a molecular mass of 6,418 +/- 2 Da. The peptide in heat stable, since full biological activity is retained after heating at 95 degrees C for 15 min, and it is destroyed by digestion with proteases. Amino acid sequence analysis revealed a high concentration of Ala and Gly residues, which respectively comprised 24 and 19% of the total amino acid content. Additionally, high levels of hydrophobic amino acids were present, accounting for the hydrophobic nature of Bac1829. Purified Bac1829 killed exponentially growing Corynebacterium renale in a dose-dependent manner by a bactericidal mode of action. A partial inhibitory spectrum analysis revealed that the following organisms were sensitive to the inhibitory activity of Bac1829: S. aureus RN4220, Streptococcus suis, Corynebacterium pseudotuberculosis, C. renale, Corynebacterium diptheriae, Haemophilus parasuis, Bordetella pertussis, Bordetella bronchoseptica, Moraxella bovis, and Pasteurella multocida. PMID:8795206

Breath analyzer screening of emergency department patients suspected of alcohol intoxication.

PubMed

Sebbane, Mustapha; Claret, Pierre-Géraud; Jreige, Riad; Dumont, Richard; Lefebvre, Sophie; Rubenovitch, Josh; Mercier, Grégoire; Eledjam, Jean-Jacques; de la Coussaye, Jean-Emmanuel

2012-10-01

Acute alcohol intoxication is a frequent cause of emergency department (ED) visits. Evaluating a patient's alcohol intoxication is commonly based on both a physical examination and determination of blood alcohol concentration (BAC). To demonstrate the feasibility and usefulness of using a last-generation infrared breath analyzer as a non-invasive and rapid screening tool for alcohol intoxication in the ED. Adult patients suspected of acute alcohol intoxication were prospectively enrolled over 10 days. Breath alcohol concentrations (BrAC) were measured using a handheld infrared breath analyzer. BAC was determined simultaneously by automated enzymatic analysis of a venous blood sample. The relationship between BAC and BrAC values was examined by both linear regression and Bland-Altman analysis. The study included 54 patients (mean age 40±14 years, sex ratio M/F of 3/1). Breath and blood alcohol concentrations ranged from 0 to 1.44 mg/L and from 0 to 4.40 g/L (0-440 mg/dL), respectively. The mean individual BAC/BrAC ratio was 2615±387, 95% confidence interval 2509-2714, which is 30% higher than the legal ratio in France (2000). The correlation between both measurements was excellent: r=0.95 (0.92-0.97). Linear regression revealed BAC=0.026+1.29 (BrAC×2000) and BAC=0.026+0.99 (BrAC×2615). Mean BAC-BrAC differences and limits of agreement were 0.49 g/L [-0.35, 1.34] (or 49 mg/dL [-35, 134] and 0.01 g/L [-0.68, 0.71] (or 1 mg/dL [-68, 71]), for the 2000 and 2615 ratios, respectively. The calculated conversion coefficient provided a satisfactory determination of blood alcohol concentration. Breath alcohol testing, using appropriate BAC/BrAC conversion, different from the legal BAC/BrAC, could be a reliable alternative for routine screening and management of alcohol intoxication in the ED. Copyright © 2012 Elsevier Inc. All rights reserved.

A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing

PubMed Central

Budiman, Muhammad A.; Mao, Long; Wood, Todd C.; Wing, Rod A.

2000-01-01

Recently a new strategy using BAC end sequences as sequence-tagged connectors (STCs) was proposed for whole-genome sequencing projects. In this study, we present the construction and detailed characterization of a 15.0 haploid genome equivalent BAC library for the cultivated tomato, Lycopersicon esculentum cv. Heinz 1706. The library contains 129,024 clones with an average insert size of 117.5 kb and a chloroplast content of 1.11%. BAC end sequences from 1490 ends were generated and analyzed as a preliminary evaluation for using this library to develop an STC framework to sequence the tomato genome. A total of 1205 BAC end sequences (80.9%) were obtained, with an average length of 360 high-quality bases, and were searched against the GenBank database. Using a cutoff expectation value of <10−6, and combining the results from BLASTN, BLASTX, and TBLASTX searches, 24.3% of the BAC end sequences were similar to known sequences, of which almost half (48.7%) share sequence similarities to retrotransposons and 7% to known genes. Some of the transposable element sequences were the first reported in tomato, such as sequences similar to maize transposon Activator (Ac) ORF and tobacco pararetrovirus-like sequences. Interestingly, there were no BAC end sequences similar to the highly repeated TGRI and TGRII elements. However, the majority (70.3%) of STCs did not share significant sequence similarities to any sequences in GenBank at either the DNA or predicted protein levels, indicating that a large portion of the tomato genome is still unknown. Our data demonstrate that this BAC library is suitable for developing an STC database to sequence the tomato genome. The advantages of developing an STC framework for whole-genome sequencing of tomato are discussed. [The BAC end sequences described in this paper have been deposited in the GenBank data library under accession nos. AQ367111–AQ368361.] PMID:10645957

Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations

PubMed Central

Heaney, Christopher D.; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R.

2015-01-01

Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI] = 1.03, 5.94) and 2.30 times (95% CI = 0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI = 1.21, 6.80) and 3.36 (95% CI = 1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. PMID:25600418

Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations.

PubMed

Heaney, Christopher D; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R

2015-04-01

Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI]=1.03, 5.94) and 2.30 times (95% CI=0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI=1.21, 6.80) and 3.36 (95% CI=1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. Copyright © 2014 Elsevier B.V. All rights reserved.

Use of bacterial artificial chromosomes in generating targeted mutations in human and mouse cytomegaloviruses.

PubMed

Borst, Eva Maria; Benkartek, Corinna; Messerle, Martin

2007-05-01

Cloning of cytomegalovirus (CMV) genomes as bacterial artificial chromosomes (BAC) in E. coli and their manipulation using the techniques of bacterial genetics has greatly facilitated the construction of CMV mutants. This unit describes easily applicable procedures that allow rapid introduction of any kind of targeted mutation into BAC-cloned CMV genomes. Protocols for the reconstitution of virus from isolated BAC DNA, preparation of a virus stock, and isolation and characterization of viral DNA are also included. Special emphasis is laid on description of critical steps and thorough characterization of the altered BACs.

Effect of biological activated carbon pre-treatment to control organic fouling in the microfiltration of biologically treated secondary effluent.

PubMed

Pramanik, Biplob Kumar; Roddick, Felicity A; Fan, Linhua

2014-10-15

Biological activated carbon (BAC) filtration was investigated as a pre-treatment for reducing the organic fouling of a microfiltration membrane (0.1 μm polyvinylidene fluoride) in the treatment of a biologically treated secondary effluent (BTSE) from a municipal wastewater treatment plant. BAC treatment of the BTSE resulted in a marked improvement in permeate flux, which was attributed to the effective removal of organic foulants and particulates. Although the BAC removed significantly less dissolved organic carbon than the granular activated carbon (GAC) treatment which was used as a control for comparison, it led to a markedly greater flux. This was attributed to the effective removal of the very high molecular weight substances such as biopolymers by the BAC through biodegradation and adsorption of those molecules on the biofilm. Size exclusion chromatography showed the BAC treatment led to approximately 30% reduction in these substances, whereas the GAC did not greatly remove these molecules. The BAC treatment led to a greater reduction of loosely-attached and firmly-attached membrane surface foulant, and this was confirmed by attenuated total reflection-fourier transform infrared spectroscopy analysis. This study demonstrated the potential of BAC pre-treatment for reducing organic fouling and thus improving flux for the microfiltration of BTSE. Copyright © 2014 Elsevier Ltd. All rights reserved.

BAC Libraries from Wheat Chromosome 7D – Efficient Tool for Positional Cloning of Aphid Resistance Genes

USDA-ARS?s Scientific Manuscript database

Positional cloning in bread wheat is a tedious task due to its huge genome size (~17 Gbp) and polyploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which make their screening very laborious. Here we pres...

The relative risk of involvement in fatal crashes as a function of race/ethnicity and blood alcohol concentration

PubMed Central

Torres, Pedro; Romano, Eduardo; Voas, Robert B.; de la Rosa, Mario; Lacey, John H.

2014-01-01

Introduction The literature presents a puzzling picture of Latinos being overrepresented in alcohol-related crashes, but not in noncrash drinking and driving. This report examines if, like other demographic variables in which some groups are at a higher crash risk than others (e.g., young drivers), different racial/ethnic groups face different crash risks Method This study compares blood-alcohol information from the 2006–2007 U.S. Fatality Analysis Reporting System (FARS) with control data from the 2007 U.S. National Roadside Survey. Logistic regression, including a dual interaction between BAC and race/ethnicity, was used to estimate crash risk at different BAC levels. Results It was found that, although Hispanic and African-American drivers were less likely to be involved in single-vehicle crashes than their White counterparts, all drivers face similar BAC relative crash risk regardless of their group membership. The overrepresentation of Latino drivers in alcohol-related crashes could be explained by differences in patterns of consumption, driving exposure, lack of awareness of driving rules, and/or socioeconomics. PMID:24529097

Energy Drinks and Alcohol: Links to Alcohol Behaviors and Consequences Across 56 Days

PubMed Central

Patrick, Megan E.; Maggs, Jennifer L.

2013-01-01

Purpose To examine short-term consequences associated with consuming alcohol and energy drinks compared with consuming alcohol without energy drinks. Methods A longitudinal measurement-burst design (14-day bursts of daily surveys in four consecutive college semesters) captured both within-person variation across occasions and between-person differences across individuals. The analytic sample of late adolescent alcohol users included 4,203 days with alcohol use across up to four semesters per person from 508 college students. Results Adding energy drink use to a given day with alcohol use was associated with an increase in number of alcoholic drinks, a trend toward more hours spent drinking, elevated estimated blood alcohol content (eBAC), a greater likelihood of subjective intoxication, and more negative consequences of drinking that day. After controlling for eBAC, energy drink use no longer predicted subjective intoxication but was still associated with a greater number of negative consequences. Conclusions The consumption of energy drinks may lead to increases in alcohol consumption and, after controlling for eBAC, negative consequences. Use of energy drinks plus alcohol represents an emerging threat to public health. PMID:24309196

Motorists' knowledge, attitudes and practices toward alcohol-impaired driving/riding in Ghana.

PubMed

Damsere-Derry, James; Palk, Gavan; King, Mark

2017-01-02

The main objective of this study was to establish the knowledge, attitudes, and practices toward drink driving/riding as a risk factor for road traffic crashes in 3 regional capitals in Ghana. The study used a face-to-face approach to randomly sample motorists who were accessing various services at fuel/gas stations, garages, and lorry terminals in 3 cities in Ghana. Over the previous 12 months, 24% of all motorists and 55% of motorists who were current alcohol users reported driving or riding a vehicle within an hour of alcohol intake. On average, motorists/riders who were current alcohol users consumed 4 standard drinks per drinking occasion. Generally, 83% of motorists who currently use alcohol walked, rode, or drove home after consuming alcohol away from their homes. Motorists/riders who reported drink driving were 4 times more likely to have had previous traffic violation arrests compared to those who reported no drink driving/riding (P =.001). Respondents were of the opinion that speeding was the major cause of traffic crashes, followed by driver carelessness, poor road conditions, inexperienced driving, and drink driving, in that order. Thirty-six percent of motorists who use alcohol had the perception that consuming between 6 and 15 standard drinks was the volume of alcohol that will take them to the legal blood alcohol concentration (BAC) limit of 0.08%. Compared to females, male motorists/riders were more likely to report drink driving (adjusted odds ratio [AOR] = 5.15; 95% confidence interval [CI], 2.31 to 11.47). Private motorists also reported a higher likelihood of drink driving compared to commercial drivers (AOR = 3.36; 95% CI, 1.88 to 6.02). Only 4% of motorists knew the legal BAC limit of Ghana and only 2% had ever been tested for drink driving/riding. The volumes of alcohol that motorists typically consume per drinking occasion were very high and their estimates of the number of drinks required to reach the legal BAC limit was also very high. Provision of authoritative information advising motorists about safe, responsible, or low-risk levels of alcohol consumption is imperative. Many traffic violations including drink driving were reported, thus suggesting a need for enhanced policing and enforcement. However, given the low level of knowledge of the legal BAC limit, educating motorists about how many drinks will approximate the legal BAC should be intensified prior to an increase in enforcement; otherwise, the desired outcome of enforcement may not be achieved.

[Diagnostic value of (18)F-FDG PET/CT for solitary nodular-type bronchoalveolar carcinoma].

PubMed

Liu, Weikun; Li, Xiangdong; Quan, Jiangtao; Ouyang, Xi; Zheng, Hui

2013-01-01

To assess the value of (18)F-FDG PET/CT in the diagnosis of solitary nodular-type bronchoalveolar carcinoma (BAC). The clinical and radiographic data were analyzed retrospectively in 30 patients with pathologically confirmed solitary nodular-type BAC who underwent (18)F-FDG PET/CT examinations between August, 2005 and December, 2006. The morphological and radioactive findings of the lesions were reviewed, and the maximum standard uptake values (SUVmax) were measured. The diagnostic accuracy of PET, PET/CT, and HRCT were analyzed. The (18)F-FDG SUV was markedly lower in BAC than in other well differentiated adenocarcinoma. In 19 of the BAC cases, PET showed a SUVmax of no less than 2.5, demonstrating positive changes. Of the total of 30 cases, 5 had ground glass opacity (GGO) changes, 3 exhibited mixed nodules with GGO changes around the lesions, and 22 cases presented with solid nodules. HRCT showed that BAC located often in the superior lobes of the bilateral lungs, mostly below the pleura in the surrounding lung field; the lesions were patchy or nodular with irregular shapes, showing lobulation in 22 cases, spiculation in 15 cases, pleural indentation in 21 cases, and vacuolar changes in 4 cases. The diagnostic accuracy of PET, PET/CT and HRCT for solitary nodular-type BAC was 36.67%, 93.33%, and 93.33%, respectively. The SUVmax of BAC provides only limited value for defining the nature of the lesions, but can serve as a general reference for assessing the disease activity. PET/CT, which allows both functional and imaging assessment, can be a valuable modality to reduce the misdiagnosis rate of BAC.

[Diagnostic value of (18)F-FDG PET/CT for solitary nodular-type bronchoalveolar carcinoma].

PubMed

Liu, Wei-Kun; Li, Xiang-Dong; Quan, Jiang-Tao; Ouyang, Xi; Zheng, Hui

2015-01-01

To assess the value of (18)F-FDG PET/CT in the diagnosis of solitary nodular-type bronchoalveolar carcinoma (BAC). The clinical and radiographic data were analyzed retrospectively in 30 patients with pathologically confirmed solitary nodular-type BAC who underwent (18)F-FDG PET/CT examinations between August, 2005 and December, 2006. The morphological and radioactive findings of the lesions were reviewed, and the maximum standard uptake values (SUVmax) were measured. The diagnostic accuracy of PET, PET/CT, and HRCT were analyzed. The (18)F-FDG SUV was markedly lower in BAC than in other well differentiated adenocarcinoma. In 19 of the BAC cases, PET showed a SUVmax of no less than 2.5, demonstrating positive changes. Of the total of 30 cases, 5 had ground glass opacity (GGO) changes, 3 exhibited mixed nodules with GGO changes around the lesions, and 22 cases presented with solid nodules. HRCT showed that BAC located often in the superior lobes of the bilateral lungs, mostly below the pleura in the surrounding lung field; the lesions were patchy or nodular with irregular shapes, showing lobulation in 22 cases, spiculation in 15 cases, pleural indentation in 21 cases, and vacuolar changes in 4 cases. The diagnostic accuracy of PET, PET/CT and HRCT for solitary nodular-type BAC was 36.67%, 93.33%, and 93.33%, respectively. The SUVmax of BAC provides only limited value for defining the nature of the lesions, but can serve as a general reference for assessing the disease activity. PET/CT, which allows both functional and imaging assessment, can be a valuable modality to reduce the misdiagnosis rate of BAC.

Evaluation of radiological and pathological prognostic factors in surgically-treated patients with bronchoalveolar carcinoma.

PubMed

Carretta, A; Canneto, B; Calori, G; Ceresoli, G L; Campagnoli, E; Arrigoni, G; Vagani, A; Zannini, P

2001-08-01

The incidence of adenocarcinoma and bronchoalveolar carcinoma has increased in recent years. The aim of this study was to retrospectively evaluate radiological and pathological factors affecting survival in patients with bronchoalveolar carcinoma (BAC) or BAC associated with adenocarcinoma who underwent surgical treatment. From May 1988 to September 1999, 49 patients with BAC or BAC and adenocarcinoma underwent surgical treatment. Complete resection was performed in 42 patients. In these patients the impact of the following factors on survival was evaluated: stage, TNM status, radiological and pathological findings (percentage of bronchoalveolar carcinoma in the tumour, presence or absence of sclerosing and mucinous patterns, vascular invasion and lymphocytic infiltration). Twenty-nine patients were male and 20 female. Mean age was 63 years. Five-year survival was 54%. Univariate analysis of the patients who underwent complete resection demonstrated a favourable impact on survival in stages Ia and Ib (P = 0.01) and in the absence of nodal involvement (P = 0.02) and mucinous patterns (P = 0.02). Mucinous pattern was also prognostically relevant at multivariate analysis (P = 0.02). In the 27 patients with stage Ia and Ib disease, univariate analysis demonstrated that the absence of mucinous pattern (P = 0.006) and a higher percentage of BAC (P = 0.01) favourably influenced survival. The latter data were also confirmed by multivariate analysis (P = 0.01). Surgical treatment of early-stage BAC and combined BAC and adenocarcinoma is associated with favourable results. However, the definition of prognostic factors is of utmost importance to improve the results of the treatment. In our series tumours of the mucinous subtype and with a lower percentage of BAC had a worse prognosis.

False-positive alarms for bacterial screening of platelet concentrates with BacT/ALERT new-generation plastic bottles: a multicenter pilot study.

PubMed

Hundhausen, T; Müller, T H

2005-08-01

The microbial detection system BacT/ALERT (bioMérieux) is widely used to monitor bacterial contamination of platelet concentrates (PCs). Recently, the manufacturer introduced polycarbonate culture bottles and a modified pH-sensitive liquid emulsion sensor as microbial growth indicator. This reconfigured assay was investigated in a routine setting. In each of eight transfusion centers, samples from 500 consecutive PCs were monitored for 1 week. For all PCs with a positive BacT/ALERT signal, retained samples and, if available, original PC containers and concomitant red blood cell concentrates were analyzed independently. Initially BacT/ALERT-positive PCs without bacterial identification in any sample were defined as false-positive. BacT/ALERT-positive PCs with bacteria in the first sample only were called potentially positive. PCs with bacteria in the first sample and the same strain in at least one additional sample were accepted as positive. Five PCs (0.13%) were positive, 9 PCs (0.23%) were potentially positive, and 35 PCs (0.9%) were false-positive. The rate of false-positive BacT/ALERT results varied substantially between centers (<0.2%-3.2%). Tracings from false-positive cultures lacked an exponential increase of the signal during incubation. Most of these false-positives were due to malfunctioning cells in various BacT/ALERT incubation units. Careful assessment of individual tracings of samples with positive signals helps to identify malfunctioning incubation units. Their early shutdown or replacement minimizes the high rate of unrectifiable product rejects attributed to false-positive alarms and avoids unnecessary concern of doctors and patients after conversion to a reconfigured BacT/ALERT assay.

Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose

PubMed Central

van Winden, Vincent J. C.; Sparrius, Marion; van de Weerd, Robert; Speer, Alexander; Ummels, Roy; Sherman, David R.

2017-01-01

The cell envelope of mycobacteria is a highly unique and complex structure that is functionally equivalent to that of Gram-negative bacteria to protect the bacterial cell. Defects in the integrity or assembly of this cell envelope must be sensed to allow the induction of stress response systems. The promoter that is specifically and most strongly induced upon exposure to ethambutol and isoniazid, first line drugs that affect cell envelope biogenesis, is the iniBAC promoter. In this study, we set out to identify the regulator of the iniBAC operon in Mycobacterium marinum using an unbiased transposon mutagenesis screen in a constitutively iniBAC-expressing mutant background. We obtained multiple mutants in the mce1 locus as well as mutants in an uncharacterized putative transcriptional regulator (MMAR_0612). This latter gene was shown to function as the iniBAC regulator, as overexpression resulted in constitutive iniBAC induction, whereas a knockout mutant was unable to respond to the presence of ethambutol and isoniazid. Experiments with the M. tuberculosis homologue (Rv0339c) showed identical results. RNAseq experiments showed that this regulatory gene was exclusively involved in the regulation of the iniBAC operon. We therefore propose to name this dedicated regulator iniBAC Regulator (IniR). IniR belongs to the family of signal transduction ATPases with numerous domains, including a putative sugar-binding domain. Upon testing different sugars, we identified trehalose as an activator and metabolic cue for iniBAC activation, which could also explain the effect of the mce1 mutations. In conclusion, cell envelope stress in mycobacteria is regulated by IniR in a cascade that includes trehalose. PMID:29281637

Generation of soluble microbial products by bio-activated carbon filter during drinking water advanced treatment and its influence on spectral characteristics.

PubMed

Shen, Hong; Chen, Xin; Zhang, Dong; Chen, Hong-Bin

2016-11-01

In order to improve our understanding of bio-activated carbon (BAC) filter, the water quality of influent and effluent treated with BAC in a drinking water treatment plant (DWTP) of Shanghai during 2015 was valued. Combining the results from UV254, SUVA254, dissolved organic carbon (DOC) and scanning electron microscopic (SEM), it is found that performance of BAC treatment will be affected by characteristics of activated carbon (AC), which is relevant to the type of activated carbon (including shape and operating time) in this study. Fluorescence excitation-emission matrix (FEEM) shows that the humification index (HIX) and index of recent autochthonous contribution (BIX) is a reliable indicator to descript the variation of dissolved organic matter (DOM) during BAC process. The pattern of variation in BIX and HIX implies that soluble microbial products (SMPs) are formed and humic-like substances are removed during BAC treatment, which is also confirmed by the change of peaks of FEEM in BAC effluent. Large, positive correlations between SUVA254 and disinfection by-products formation potential yield (DBPFP yield) demonstrate that UV-absorbing DOM is directly related to the generation of DBPs. Poor correlations of HIX with DBPFP suggest that non-humic substances with UV-absorbing properties play an important role in the generation of DBPs in water with low SUVA254. Finally, strong but negative correlations between BIX and DBPFP suggest that vigorous microbial metabolism of BAC results in a decrease in DBPFP. However, the DBPFP yield will be enhanced for the generation of SMPs by BAC, especially in summer. Copyright © 2016 Elsevier B.V. All rights reserved.

Endocrine cells in the denervated intestine

PubMed Central

Santos, Gilda C; Zucoloto, Sérgio; Garcia, Sérgio B

2000-01-01

This study deals with the effects of myenteric denervation of the proximal jejunum on endocrine cell population of the crypt-villus unit, 5 months after treatment with benzalkonium chloride (BAC). Male Wistar albino rats weighing on average 100 g were allocated to two groups: the BAC group − the proximal jejunal serosa was treated with 2 mm BAC for 30 min, and the control group − treated with saline solution (0,9% NaCl). There was a significant reduction in neurone number in the jejunal myenteric plexus of the BAC group and the endocrine cell population (serotoninergic and argyrophilic cells) was significantly increased in this intestine segment. In conclusion, the present findings provide further evidence that the myenteric denervation induced by BAC may lead to the development of a local imbalance of the neurotransmitters, with a consequent induction of enteroendocrine cell (argyrophilic and serotoninergic cells) hyperplasia in the crypt and villus. PMID:10971748

Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuskan, Gerald A; Gunter, Lee E; DiFazio, Stephen P

The 18S-28S rDNA and 5S rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 18S-28S rDNA sites and one 5S rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis -type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 chromosomes, as expected. BACs from LG-I hybridized to the longest chromosome in the complement. All BAC positions were found to be concordant with sequencemore » assembly positions. BAC-FISH will be useful for delineating each of the Populus trichocarpa chromosomes and improving the sequence assembly of this model angiosperm tree species.« less

Blood alcohol concentration in drivers of Liege area (Belgium): a 5-year analysis.

PubMed

Deville, M; Charlier, C

2015-10-01

The objective of the study was to describe 'the results of the blood alcohol determinations made on drivers from the Liege area between 2007 and 2012. The results were interpreted according to the sex, to the age, to the circumstances and temporal variation of the test. Statistical analysis was performed using R® software. 2725 determinations were done, mainly after crashes. The mean blood alcohol concentration (BAC) was 1.69 g/L, and 2132 drivers were above the legal threshold. A majority of offenders were men, but the mean BAC did not differ significantly between men and women. A correlation between age and mean BAC can be observed on the positive cases. Lowest and highest mean BACs are observed during the daytime and during the night, respectively, but no significant difference can be observed between the week and the weekend. Finally, no significant difference in BAC was observed over years.

Alcohol-impaired speed and accuracy of cognitive functions: a review of acute tolerance and recovery of cognitive performance.

PubMed

Schweizer, Tom A; Vogel-Sprott, Muriel

2008-06-01

Much research on the effects of a dose of alcohol has shown that motor skills recover from impairment as blood alcohol concentrations (BACs) decline and that acute tolerance to alcohol impairment can develop during the course of the dose. Comparable alcohol research on cognitive performance is sparse but has increased with the development of computerized cognitive tasks. This article reviews the results of recent research using these tasks to test the development of acute tolerance in cognitive performance and recovery from impairment during declining BACs. Results show that speed and accuracy do not necessarily agree in detecting cognitive impairment, and this mismatch most frequently occurs during declining BACs. Speed of cognitive performance usually recovers from impairment to drug-free levels during declining BACs, whereas alcohol-increased errors fail to diminish. As a consequence, speed of cognitive processing tends to develop acute tolerance, but no such tendency is shown in accuracy. This "acute protracted error" phenomenon has not previously been documented. The findings pose a challenge to the theory of alcohol tolerance on the basis of physiological adaptation and raise new research questions concerning the independence of speed and accuracy of cognitive processes, as well as hemispheric lateralization of alcohol effects. The occurrence of alcohol-induced protracted cognitive errors long after speed returned to normal is identified as a potential threat to the safety of social drinkers that requires urgent investigation.

Rapid identification of bacteria in positive blood culture by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Schmidt, V; Jarosch, A; März, P; Sander, C; Vacata, V; Kalka-Moll, W

2012-03-01

Blood culture is probably the most significant specimen used for the diagnosis of bacterial infections, especially for bloodstream infections. In the present study, we compared the resin-containing BD BACTEC™ Plus-Aerobic (Becton Dickinson), non-charcoal-containing BacT/Alert(®) SA (bioMérieux), and charcoal-containing BacT/Alert(®) FA (bioMérieux) blood culture bottles with direct identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 103 bacterial isolates, from clinical blood cultures, representing the most frequent 13 genera and 24 species were examined. Bacteria were extracted from positive blood culture broth by density centrifugation and then subjected to identification by MALDI-TOF MS using two different volumes and chemical treatments. Overall, correct identification by MALDI-TOF MS was obtained for the BD BACTEC™ Plus-Aerobic, BacT/Alert(®) SA, and BacT/Alert(®) FA blood culture bottles in 72%, 45.6%, and 23%, respectively, for gram-negative bacteria in 86.6%, 69.2%, and 47.1%, respectively, and for gram-positive bacteria in 60.0%, 28.8%, and 5.4%, respectively. The lack of identification was observed mainly with viridans streptococci. Depending on the blood culture bottles used in routine diagnostic procedures and the protocol for bacterial preparation, the applied MALDI-TOF MS represents an efficient and rapid method for direct bacterial identification.

Influence of the Fight BAC! food safety campaign on an urban Latino population in Connecticut.

PubMed

Dharod, Jigna Morarji; Perez-Escamilla, Rafael; Bermudez-Millan, Angela; Segura-Perez, Sofia; Damio, Grace

2004-01-01

To assess the coverage and consumer satisfaction with the Fight BAC! campaign and to evaluate the influence of the campaign on food safety knowledge, attitudes, and behaviors among a predominantly Latino population living in inner-city Hartford, Connecticut. A cross-sectional pre- and post-survey was administered to 500 Latino consumers in either English or Spanish. It included 30 food safety-related questions and information on the socioeconomic and demographic characteristics of participants. Respondents were selected from Latino households, with at least one child 12 years old or under, located in 5 predominantly Latino neighborhoods in inner-city Hartford. Fight BAC! media campaign. Seventy-three percent of respondents were exposed to at least one campaign media item and were highly satisfied with it. Recognition of the Fight BAC! logo increased from 10% to 42% between surveys (P <.001). Individuals exposed to the campaign were more likely to have a food safety knowledge score of at least 2 of a possible 4 compared with unexposed counterparts (odds ratio = 3.54; 95% CI 1.74-7.18; P <.001). They were also more likely to report defrosting meats in the refrigerator (14% vs 7%; P =.01). There was a dose-response association between the degree of campaign exposure and awareness of the term "cross-contamination." Social marketing campaigns that take advantage of multiple culturally relevant media channels are likely to improve food safety awareness and bring about changes in food safety knowledge and attitudes among Latino consumers.

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecul...

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

USDA-ARS?s Scientific Manuscript database

Background: BAC-based physical maps provide for sequencing across an entire genome or selected sub-genome regions of biological interest. Using the minimum tiling path as a guide, it is possible to select specific BAC clones from prioritized genome sections such as a genetically defined QTL interv...

DNA sequences and composition from 12 BAC clones-derived MUSB SSR markers mapped to cotton (Gossypium Hirsutum L. x G. Barbadense L.)chromosomes 11 and 21

USDA-ARS?s Scientific Manuscript database

To discover resistance (R) and/or pathogen-induced (PR) genes involved in disease response, 12 bacterial artificial chromosome (BAC) clones from cv. Acala Maxxa (G. hirsutum) were sequenced at the Clemson University, Genomics Institute, Clemson, SC. These BACs derived MUSB single sequence repeat (SS...

Germ-line transformation of the Queensland fruit fly, Bactrocera tryoni, using a piggyBac vector in the presence of endogenous piggyBac elements

USDA-ARS?s Scientific Manuscript database

We report the stable genetic transformation of the Queensland fruit fly Bactrocera tryoni using a piggyBac vector marked with either the fluorescent protein DsRed or EGFP.A transformation frequency of 5–10% was obtained.Inheritance of the transgenes has remained stable over eight generations despite...

Blood alcohol concentration measurement using a salivary reagent stick: a reliable tool for emergency departments?

PubMed

Phair, I C; Mardel, S; Bodiwala, G G

1990-06-01

Measurements of blood alcohol concentration (BAC) were made on patients who presented to an accident and emergency department with acute alcohol intoxication. A correlation of r = 0.418 was noted to exist between BAC as measured by sampling saliva and blood. Blood alcohol concentrations as measured by salivary reagent strip (ALCO-SCREEN, Chem Elec.) were significantly lower (p less than 0.0001) than those determined by gas chromatography of serum. Although such reagent strips offer a rapid measurement of BAC, it is concluded that they are unreliable for the quantitative measurement of BAC in accident and emergency departments.

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

Detection of iso-α-acids to confirm beer consumption in postmortem specimens.

PubMed

Rodda, Luke N; Gerostamoulos, Dimitri; Drummer, Olaf H

2015-01-01

Iso-α-acids (IAAs) can be used as markers for the consumption of beer. Postmortem specimens from a range of coronial cases were analyzed for IAAs in order to determine the prevalence of beer consumption and any correlation to blood alcohol concentrations (BAC). A total of 130 cases were included in this study including those where beer was mentioned in the case circumstances, cases where beer was not mentioned specifically but alcohol was detected, and cases where neither beer was mentioned nor a positive BAC was present. Available blood, serum, vitreous humour and urine specimens were analyzed. Of the 50 cases where beer was mentioned, 86% had one or more IAAs detected. In cases that only had a positive BAC (n = 60), 57% of these cases also showed the presence of these beer markers. IAAs were detected in specimens obtained from traumatized, burnt, and decomposed cases with a mention of beer consumption or where BAC was positive in blood. No IAAs were detected in cases where BAC was negative. There was little or no correlation between blood IAA concentrations and BAC. This study demonstrates the possible detection of IAAs as a marker for beer consumption. Copyright © 2014 John Wiley & Sons, Ltd.

Molecular Dynamics Simulations of KirBac1.1 Mutants Reveal Global Gating Changes of Kir Channels.

PubMed

Linder, Tobias; Wang, Shizhen; Zangerl-Plessl, Eva-Maria; Nichols, Colin G; Stary-Weinzinger, Anna

2015-04-27

Prokaryotic inwardly rectifying (KirBac) potassium channels are homologous to mammalian Kir channels. Their activity is controlled by dynamical conformational changes that regulate ion flow through a central pore. Understanding the dynamical rearrangements of Kir channels during gating requires high-resolution structure information from channels crystallized in different conformations and insight into the transition steps, which are difficult to access experimentally. In this study, we use MD simulations on wild type KirBac1.1 and an activatory mutant to investigate activation gating of KirBac channels. Full atomistic MD simulations revealed that introducing glutamate in position 143 causes significant widening at the helix bundle crossing gate, enabling water flux into the cavity. Further, global rearrangements including a twisting motion as well as local rearrangements at the subunit interface in the cytoplasmic domain were observed. These structural rearrangements are similar to recently reported KirBac3.1 crystal structures in closed and open conformation, suggesting that our simulations capture major conformational changes during KirBac1.1 opening. In addition, an important role of protein-lipid interactions during gating was observed. Slide-helix and C-linker interactions with lipids were strengthened during activation gating.

Development of the piggyBac transposable system for Plasmodium berghei and its application for random mutagenesis in malaria parasites

PubMed Central

2011-01-01

Background The genome of a number of species of malaria parasites (Plasmodium spp.) has been sequenced in the hope of identifying new drug and vaccine targets. However, almost one-half of predicted Plasmodium genes are annotated as hypothetical and are difficult to analyse in bulk due to the inefficiency of current reverse genetic methodologies for Plasmodium. Recently, it has been shown that the transposase piggyBac integrates at random into the genome of the human malaria parasite P. falciparum offering the possibility to develop forward genetic screens to analyse Plasmodium gene function. This study reports the development and application of the piggyBac transposition system for the rodent malaria parasite P. berghei and the evaluation of its potential as a tool in forward genetic studies. P. berghei is the most frequently used malaria parasite model in gene function analysis since phenotype screens throughout the complete Plasmodium life cycle are possible both in vitro and in vivo. Results We demonstrate that piggyBac based gene inactivation and promoter-trapping is both easier and more efficient in P. berghei than in the human malaria parasite, P. falciparum. Random piggyBac-mediated insertion into genes was achieved after parasites were transfected with the piggyBac donor plasmid either when transposase was expressed either from a helper plasmid or a stably integrated gene in the genome. Characterization of more than 120 insertion sites demonstrated that more than 70 most likely affect gene expression classifying their protein products as non-essential for asexual blood stage development. The non-essential nature of two of these genes was confirmed by targeted gene deletion one of which encodes P41, an ortholog of a human malaria vaccine candidate. Importantly for future development of whole genome phenotypic screens the remobilization of the piggyBac element in parasites that stably express transposase was demonstrated. Conclusion These data demonstrate that piggyBac behaved as an efficient and random transposon in P. berghei. Remobilization of piggyBac element shows that with further development the piggyBac system can be an effective tool to generate random genome-wide mutation parasite libraries, for use in large-scale phenotype screens in vitro and in vivo. PMID:21418605

Working memory impairment in probands with schizoaffective disorder and first degree relatives of schizophrenia probands extend beyond deficits predicted by generalized neuropsychological impairment.

PubMed

Kristian Hill, S; Buchholz, Alison; Amsbaugh, Hayley; Reilly, James L; Rubin, Leah H; Gold, James M; Keefe, Richard S E; Pearlson, Godfrey D; Keshavan, Matcheri S; Tamminga, Carol A; Sweeney, John A

2015-08-01

Working memory impairment is well established in psychotic disorders. However, the relative magnitude, diagnostic specificity, familiality pattern, and degree of independence from generalized cognitive deficits across psychotic disorders remain unclear. Participants from the Bipolar and Schizophrenia Network on Intermediate Phenotypes (B-SNIP) study included probands with schizophrenia (N=289), psychotic bipolar disorder (N=227), schizoaffective disorder (N=165), their first-degree relatives (N=315, N=259, N=193, respectively), and healthy controls (N=289). All were administered the WMS-III Spatial Span working memory test and the Brief Assessment of Cognition in Schizophrenia (BACS) battery. All proband groups displayed significant deficits for both forward and backward span compared to controls. However, after covarying for generalized cognitive impairments (BACS composite), all proband groups showed a 74% or greater effect size reduction with only schizoaffective probands showing residual backward span deficits compared to controls. Significant familiality was seen in schizophrenia and bipolar pedigrees. In relatives, both forward and backward span deficits were again attenuated after covarying BACS scores and residual backward span deficits were seen in relatives of schizophrenia patients. Overall, both probands and relatives showed a similar pattern of robust working memory deficits that were largely attenuated when controlling for generalized cognitive deficits. Copyright © 2015 Elsevier B.V. All rights reserved.

Testing chromosomal phylogenies and inversion breakpoint reuse in Drosophila. The martensis cluster revisited.

PubMed

Prada, Carlos F; Delprat, Alejandra; Ruiz, Alfredo

2011-02-01

The chromosomal relationships of the four martensis cluster species are among the most complex and intricate within the entire Drosophila repleta group, due to the so-called sharing of inversions. Here, we have revised these relationships using comparative mapping of bacterial artificial chromosome (BAC) clones on the salivary gland chromosomes. A physical map of chromosome 2 of Drosophila uniseta (one of the cluster members) was generated by in situ hybridization of 82 BAC clones from the physical map of the Drosophila buzzatii genome (an outgroup that represents the ancestral arrangement). By comparing the marker positions, we determined the number, order, and orientation of conserved chromosomal segments between chromosome 2 of D. buzzatii and D. uniseta. GRIMM software was used to infer that a minimum of five chromosomal inversions are necessary to transform the chromosome 2 of D. buzzatii into that of D. uniseta. Two of these inversions have been overlooked in previous cytological analyses. The five fixed inversions entail two breakpoint reuses because only nine syntenic segments and eight interruptions were observed. We tested for the presence of the five inversions fixed in D. uniseta in the other three species of the martensis cluster by in situ hybridization of eight breakpoint-bearing BAC clones. The results shed light on the chromosomal phylogeny of the martensis cluster, yet leave a number of questions open.

Arterial function of carotid and brachial arteries in postmenopausal vegetarians.

PubMed

Su, Ta-Chen; Torng, Pao-Ling; Jeng, Jiann-Shing; Chen, Ming-Fong; Liau, Chiau-Suong

2011-01-01

Vegetarianism is associated with a lower risk of cardiovascular disease. However, studies of arterial function in vegetarians are limited. This study investigated arterial function in vegetarianism by comparing 49 healthy postmenopausal vegetarians with 41 age-matched omnivores. The arterial function of the common carotid artery was assessed by carotid duplex, while the pulse dynamics method was used to measure brachial artery distensibility (BAD), compliance (BAC), and resistance (BAR). Fasting blood levels of glucose, lipids, lipoprotein (a), high-sensitivity C-reactive protein, homocysteine, and vitamin B12 were also measured. Vegetarians had significantly lower serum cholesterol, high-density and low-density lipoprotein, and glucose compared with omnivores. They also had lower vitamin B12 but higher homocysteine levels. Serum levels of lipoprotein (a) and high-sensitivity C-reactive protein were no different between the two groups. There were no significant differences in carotid beta stiffness index, BAC, and BAD between the two groups even after adjustment for associated covariates. However, BAR was significantly lower in vegetarians than in omnivores. Multiple linear regression analysis revealed that age and pulse pressure were two important determinants of carotid beta stiffness index and BAD. Vegetarianism is not associated with better arterial elasticity. Apparently healthy postmenopausal vegetarians are not significantly better in terms of carotid beta stiffness index, BAC, and BAD, but have significantly decreased BAR than omnivores. Prevention of vitamin B12 deficiency might be beneficial for cardiovascular health in vegetarians.

Prevalence of alcohol-impaired driving and riding in northern Ghana.

PubMed

Damsere-Derry, James; Palk, Gavan; King, Mark

2016-01-01

The objective of this study was to determine the roadside prevalence of alcohol-impaired driving among drivers and riders in northern Ghana. The study also verifies motorists' perceptions of their own alcohol use and knowledge of the legal blood alcohol concentration (BAC) limit in Ghana. With the assistance of police, systematic random sampling was used to collect data at roadblocks using a cross-sectional study design. Breathalyzers were used to screen whether motorists had detectable alcohol in their breath and follow-up breath tests were conducted to measure the actual breath alcohol levels among positive participants. In all, 9.7% of the 789 participants had detectable alcohol, among whom 6% exceeded the legal BAC limit of 0.08%. The prevalence of alcohol-impaired driving/riding was highest among cyclists (10% of all cyclists breath-tested) followed by truck drivers (9%) and motorcyclists (7% of all motorcyclists breath-tested). The occurrence of a positive BAC among cyclists was about 8 times higher (odds ratio [OR] = 7.73; P < .001) and it was 2 times higher among motorcyclists (OR = 2.30; P = .039) compared to private car drivers. The likelihood for detecting a positive BAC among male motorists/riders was higher than that among females (OR = 1.67; P = .354). The odds for detecting a positive BAC among weekend motorists/riders was significantly higher than on weekdays (OR = 2.62; P = .001). Alcohol-impaired driving/riding in Ghana is high by international standards. In order to attenuate the harmful effects of alcohol misuse such as alcohol-impaired driving/riding, there is the need to educate road users about how much alcohol they can consume and stay below the legal limit. The police should also initiate random breath testing to instill the deterrence of detection, certainty of apprehension and punishment, and severity and celerity of punishment among drink-driving motorists and riders.

Prevalence of alcohol among nonfatally injured road accident casualties in two level III trauma centers in northern Ghana.

PubMed

Damsere-Derry, James; Palk, Gavan; King, Mark

2018-02-17

Alcohol use is pervasive among motorists on the road in Ghana; however, we do not know the extent to which this behavior is implicated in road accidents in this country. The main objective of this research was to establish the prevalence of alcohol in the blood of nonfatally injured casualties in the emergency departments (EDs) in northern Ghana. Participants were injured road traffic crash victims, namely, pedestrians, cyclists, motorcyclists, and drivers seeking treatment at an ED. The study sites were 2 level III trauma centers located in Wa and Bolgatanga. Participants were screened for alcohol followed by breath tests for positive participants using breathalyzers. Two hundred and sixty-two accident victims visited EDs, 58% of whom were in Wa. Among the victims, 41% were hospitalized and 57% experienced slight injuries. The vast majority (76%) of the casualties were motorcyclists, 13% were pedestrians, 8% were cyclists, and 2% were drivers. Casualties who had detectable alcohol in their blood were predominantly vulnerable road users. In all, 34% of participants had detectable blood alcohol concentrations (BACs) and the mean BAC for all casualties who tested positive and could give definitive BACs was 0.2265 (226 mg/dl). The prevalence of alcohol use was 53% among cyclists, 34% among motorcyclists, 21% among pedestrians, and 17% among drivers. Male casualties were more likely to test positive for alcohol than females. In addition, the prevalence of alcohol was significantly higher among injured casualties in Bolgatanga compared to Wa. There was a high prevalence of alcohol use among nonfatally injured casualties in northern Ghana and injury severity increased with BAC. AUDIT screening in the hospital, alcohol consumption guideline, road safety education with an emphasis on minimizing or eliminating alcohol consumption, and enhanced enforcement of the BAC limit among motorists are recommended.

Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources.

PubMed

Raith, Meredith R; Kelty, Catherine A; Griffith, John F; Schriewer, Alexander; Wuertz, Stefan; Mieszkin, Sophie; Gourmelon, Michele; Reischer, Georg H; Farnleitner, Andreas H; Ervin, Jared S; Holden, Patricia A; Ebentier, Darcy L; Jay, Jennifer A; Wang, Dan; Boehm, Alexandria B; Aw, Tiong Gim; Rose, Joan B; Balleste, E; Meijer, W G; Sivaganesan, Mano; Shanks, Orin C

2013-11-15

The State of California has mandated the preparation of a guidance document on the application of fecal source identification methods for recreational water quality management. California contains the fifth highest population of cattle in the United States, making the inclusion of cow-associated methods a logical choice. Because the performance of these methods has been shown to change based on geography and/or local animal feeding practices, laboratory comparisons are needed to determine which assays are best suited for implementation. We describe the performance characterization of two end-point PCR assays (CF128 and CF193) and five real-time quantitative PCR (qPCR) assays (Rum2Bac, BacR, BacCow, CowM2, and CowM3) reported to be associated with either ruminant or cattle feces. Each assay was tested against a blinded set of 38 reference challenge filters (19 duplicate samples) containing fecal pollution from 12 different sources suspected to impact water quality. The abundance of each host-associated genetic marker was measured for qPCR-based assays in both target and non-target animals and compared to quantities of total DNA mass, wet mass of fecal material, as well as Bacteroidales, and enterococci determined by 16S rRNA qPCR and culture-based approaches (enterococci only). Ruminant- and cow-associated genetic markers were detected in all filters containing a cattle fecal source. However, some assays cross-reacted with non-target pollution sources. A large amount of variability was evident across laboratories when protocols were not fixed suggesting that protocol standardization will be necessary for widespread implementation. Finally, performance metrics indicate that the cattle-associated CowM2 qPCR method combined with either the BacR or Rum2Bac ruminant-associated methods are most suitable for implementation. Published by Elsevier Ltd.

The Major Portal of Entry of Koi Herpesvirus in Cyprinus carpio Is the Skin▿

PubMed Central

Costes, B.; Raj, V. Stalin; Michel, B.; Fournier, G.; Thirion, M.; Gillet, L.; Mast, J.; Lieffrig, F.; Bremont, M.; Vanderplasschen, A.

2009-01-01

Koi herpesvirus (KHV), recently designated Cyprinid herpesvirus 3, is the causative agent of a lethal disease in koi and common carp. In the present study, we investigated the portal of entry of KHV in carp by using bioluminescence imaging. Taking advantage of the recent cloning of the KHV genome as a bacterial artificial chromosome (BAC), we produced a recombinant plasmid encoding a firefly luciferase (LUC) expression cassette inserted in the intergenic region between open reading frame (ORF) 136 and ORF 137. Two viral strains were then reconstituted from the modified plasmid, the FL BAC 136 LUC excised strain and the FL BAC 136 LUC TK revertant strain, including a disrupted and a wild-type thymidine kinase (TK) locus, respectively. In vitro, the two recombinant strains replicated comparably to the parental FL strain. The FL BAC 136 LUC TK revertant strain was shown in vitro to induce a bioluminescent signal allowing the detection of single positive cells as early as 24 h postinfection, while in vivo, it induced KHV infection in carp that was indistinguishable from that induced by the parental FL strain. To identify the KHV portal of entry, carp were analyzed by bioluminescence imaging at different times postinfection with the FL BAC 136 LUC TK revertant strain. These analyses demonstrated that the skin of the fish covering the fins and also the body is the major portal of entry for KHV in carp. Finally, to further demonstrate the role of the skin as the KHV portal of entry, we constructed an original system, nicknamed “U-tube,” to perform percutaneous infection restricted to the posterior part of the fish. All the data obtained in the present study demonstrate that the skin, and not the gills, is the major portal of entry for KHV in carp. PMID:19153228

Therapeutic Effects of Sodium Hyaluronate on Ocular Surface Damage Induced by Benzalkonium Chloride Preserved Anti-glaucoma Medications

PubMed Central

Liu, Xing; Yu, Fen-Fen; Zhong, Yi-Min; Guo, Xin-Xing; Mao, Zhen

2015-01-01

Background: Long-term use of benzalkonium chloride (BAC)-preserved drugs is often associated with ocular surface toxicity. Ocular surface symptoms had a substantial impact on the glaucoma patients’ quality of life and compliance. This study aimed to investigate the effects of sodium hyaluronate (SH) on ocular surface toxicity induced by BAC-preserved anti-glaucoma medications treatment. Methods: Fifty-eight patients (101 eyes), who received topical BAC-preserved anti-glaucoma medications treatment and met the severe dry eye criteria, were included in the analysis. All patients were maintained the original topical anti-glaucoma treatment. In the SH-treated group (56 eyes), unpreserved 0.3% SH eye drops were administered with 3 times daily for 90 days. In the control group (55 eyes), phosphate-buffered saline were administered with 3 times daily for 90 days. Ocular Surface Disease Index (OSDI) questionnaire, break-up time (BUT) test, corneal fluorescein staining, corneal and conjunctival rose Bengal staining, Schirmer test, and conjunctiva impression cytology were performed sequentially on days 0 and 91. Results: Compared with the control group, SH-treated group showed decrease in OSDI scores (Kruskal-Wallis test: H = 38.668, P < 0.001), fluorescein and rose Bengal scores (Wilcoxon signed-ranks test: z = −3.843, P < 0.001, and z = −3.508, P < 0.001, respectively), increase in tear film BUT (t-test: t = −10.994, P < 0.001) and aqueous tear production (t-test: t = −10.328, P < 0.001) on day 91. The goblet cell density was increased (t-test: t = −9.981, P < 0.001), and the morphology of the conjunctival epithelium were also improved after SH treatment. Conclusions: SH significantly improved both symptoms and signs of ocular surface damage in patients with BAC-preserved anti-glaucoma medications treatment. SH could be proposed as a new attempt to reduce ocular surface toxicity, and alleviate symptoms of ocular surface damage in BAC-preserved anti-glaucoma medications treatment. PMID:26365960

A study into blood alcohol concentration in fatal accidents among vulnerable road users in a tertiary care hospital Sri Lanka.

PubMed

Edirisinghe, Anuruddhi Samanthika; Kitulwatte, Indira Deepthi; Senarathne, Udara Dilrukshi

2015-01-01

Reckless driving behaviour associated with alcohol has been well known. In Sri Lanka, research on blood alcohol concentration (BAC) in road fatalities is scares. Thus, we studied the BAC in vulnerable road users (VRUs) encountered in medico-legal autopsies. A retrospective descriptive study based on case records of VRU fatalities from 2005 to 2012 referred for a tertiary care unit for post-mortem examination was conducted. A pro-forma was developed to extract data from the post-mortem blood alcohol reports. Data were analysed using percentages and p-values. There were 119 cases from the 328 autopsies to investigate blood alcohol tests. A total of 51% (n = 61) out of 119 had BAC above 80 mg/100 ml and mean level was 103 mg/100 ml. 2/3 of pedestrians had a BAC above 80 mg/100 ml with a mean level of 139 mg/dl. The highest mean blood alcohol (158 mg/dl) was reported from three-wheeler users. Majority of cases with more than 80 mg/100 ml BAC was reported in the age group of 40-60 years, while 40% of the elderly too had a BAC above 80 mg/100 ml. The comparison between pedestrians having above 80 mg/100 ml of BAC with that of other VRUs (active road users) showed a significant statistical difference (p = 0.017). The study results suggest that alcohol influence among pedestrians represent a significant risk factor for fatal road traffic accidents.

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

PubMed

Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S S; Kudrna, David A; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A; Luo, Meizhong

2013-11-01

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

The role of alcohol in road traffic accidents with fatal outcome: 10-year period in Croatia Split-Dalmatia County.

PubMed

Sutlovic, Davorka; Scepanovic, Antonija; Bosnjak, Marinko; Versic-Bratincevic, Maja; Definis-Gojanovic, Marija

2014-01-01

The aim of the study was to investigate the relationship between alcohol consumption and fatal road traffic accidents that took place in Split-Dalmatia County (Croatia) during a 10-year period (from August 2001 to August 2011). A retrospective analysis of 474 autopsy reports was performed, with an emphasis on 337 toxicologal findings of blood alcohol concentration (BAC) and the mode of participation in traffic (driver, passenger, pedestrian, or cyclist). Relations between the BAC, the weekday on which death occurred, victim's age and gender, and differences according to 3 successive legislation periods within the observed time frame were analyzed. The BAC was measured by gas chromatography with headspace and flame ionization detection. Alcohol was regarded as a contributive death factor if BAC was positive; that is, higher than 0.5 g/kg. BAC was positive in 177 cases. Most often it was the car driver who had a positive BAC. Victims of traffic accidents were mostly male drivers, and those accidents were more often associated with alcohol consumption. Consumption of alcohol produced a significant increase in culpability. The results of our study show that alcohol remains one of the main contributing factors of traffic accidents in Split-Dalmatia County. Unfortunately, legislation changes regarding the allowed BAC did not cause any reduction in casualties among drivers driving under the influence of alcohol (DUIA). Chi-square test of the number of total driver victims and driver victims who were DUIA revealed no significant difference (P = .173).

Distinct Effect of Benzalkonium Chloride on the Esterase and Aryl Acylamidase Activities of Butyrylcholinesterase.

PubMed

Jaganathan; Boopathy

2000-08-01

Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) from vertebrates, other than their predominant acylcholine hydrolase (esterase) activity, display a genuine aryl acylamidase activity (AAA) capable of hydrolyzing the synthetic substrate o-nitroacetanilide to o-nitroaniline. This AAA activity is strongly inhibited by classical cholinesterase (ChE) inhibitors. In the present study, benzalkonium chloride (BAC), a cationic detergent widely used as a preservative in pharmaceutical preparations, has been shown to distinctly modulate the esterase and AAA activities of BChEs. The detergent BAC was able to inhibit the esterase activity of human serum and horse serum BChEs and AChEs from electric eel and human erythrocyte. The remarkable property of BAC was its ability to profoundly activate the AAA activity of human serum and horse serum BChEs but not the AAA activity of AChEs. Thus BAC seem to preferentially activate the AAA activity of BChEs alone. Results of the study using the ChE active site-specific inhibitor diisopropyl phosphorofluoridate indicated that BAC binds to the active site of ChEs. Furthermore, studies using a structural homolog of BAC indicated that the alkyl group of BAC is essential not only for its interaction with ChEs but also for its distinct effect on the esterase and AAA activities of BChEs. This is the first report of a compound that inhibits the esterase activity, while simultaneously activating the AAA activity, of BChEs. Copyright 2000 Academic Press.

The canine sarcoglycan delta gene: BAC clone contig assembly, chromosome assignment and interrogation as a candidate gene for dilated cardiomyopathy in Dobermann dogs.

PubMed

Stabej, P; Leegwater, P A J; Imholz, S; Versteeg, S A; Zijlstra, C; Stokhof, A A; Domanjko-Petriè, A; van Oost, B A

2005-01-01

Dilated cardiomyopathy (DCM) is a common disease of the myocardium recognized in human, dog and experimental animals. Genetic factors are responsible for a large proportion of cases in humans, and 17 genes with DCM causing mutations have been identified. The genetic origin of DCM in the Dobermann dogs has been suggested, but no disease genes have been identified to date. In this paper, we describe the characterization and evaluation of the canine sarcoglycan delta (SGCD), a gene implicated in DCM in human and hamster. Bacterial artificial chromosomes (BACs) containing the canine SGCD gene were isolated with probes for exon 3 and exons 4-8 and were characterized by Southern blot analysis. BAC end sequences were obtained for four BACs. Three of the BACs overlapped and could be ordered relative to each other and the end sequences of all four BACs could be anchored on the preliminary assembly of the dog genome sequence (www. ensembl.org). One of the BACs of the partial contig was localized by fluorescent in situ hybridization to canine chromosome 4q22, in agreement with the dog genome sequence. Two highly informative polymorphic microsatellite markers in intron 7 of the SGCD gene were identified. In 25 DCM-affected and 13 non DCM-affected dogs seven different haplotypes could be distinguished. However, no association between any of the SGCD variants and the disease locus was apparent.

Alcohol Involvement in Homicide Victimization in the U.S

PubMed Central

Naimi, Timothy S.; Xuan, Ziming; Cooper, Susanna E.; Coleman, Sharon M.; Hadland, Scott E.; Swahn, Monica H.; Heeren, Timothy C.

2016-01-01

Background Although the association between alcohol and homicide is well documented, there has been no recent study of alcohol involvement in homicide victimization in U.S. states. The objective of this paper was to determine the prevalence of alcohol involvement in homicide victimization and identify socio-demographic and other factors associated with alcohol involvement in homicide victimization. Methods Data from homicide victims with a reported blood alcohol content (BAC) level were analyzed from 17 states from 2010–12 using the National Violent Death Reporting System. Logistic regression was used to investigate factors associated with the odds of homicide victims having a BAC ≥0.08%. Results Among all homicide victims, 39.9% had a positive BAC including 13.7% with a BAC between 0.01%–0.79% and 26.2% of victims with a BAC ≥0.08%. Males were twice as likely as females to have a BAC ≥0.08% (29.1% vs. 15.2%; p < 0.001). Characteristics that were independent predictors of homicide victims having a BAC ≥0.08 included male sex, American Indian/Alaska Native race, Hispanic ethnicity, history of intimate partner violence, and non-firearm homicides. Conclusions Alcohol is present in a substantial proportion of homicide victims in the U.S., with substantial variation by state, demographic and circumstantial characteristics. Future studies should explore the relationships between state-level alcohol policies and alcohol-involvement among perpetrators and victims of homicide. PMID:27676334

What Should We Do When Participants Report Dangerous Drinking? The Impact of Personalized Letters Versus General Pamphlets as a Function of Sex and Controlled Orientation.

PubMed

Neighbors, Clayton; Pedersen, Eric R; Kaysen, Debra; Kulesza, Magdalena; Walter, Theresa

Research in which participants report potentially dangerous health-related behaviors raises ethical and professional questions about what to do with that information. Policies and laws regarding reportable behaviors vary across states and Institutional Review Boards (IRB). In alcohol research, IRBs often require researchers to respond to participants who report dangerous drinking practices. Researchers have little guidance regarding how best to respond in such cases. Personalized feedback or general nonpersonalized information may prove differentially effective as a function of gender and/or level of self-determination. This study evaluated response strategies for reducing peak blood alcohol concentration (BAC) among participants reporting dangerous BACs (≥ .35%) in the context of a two-year longitudinal intervention trial with 818 heavy drinking college students. After each assessment, participants who reported drinking to estimated BACs at or greater than .35% were sent either a personalized letter expressing concern and indicating their reported BAC or a nonpersonalized pamphlet that included general information about alcohol and other substances, referral information, and a BAC handout. Hierarchical linear modeling results revealed that both strategies were associated with reduced peak BAC when controlling for previous BAC. The personalized letter was more effective for women and for students who tend to regulate their behavior based on others' expectations and contingencies in the environment. This research provides some guidance for researchers considering appropriate responses to participants who report dangerous health behavior in the context of a research trial.

Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus.

PubMed

Ollitrault, Frédérique; Terol, Javier; Pina, Jose Antonio; Navarro, Luis; Talon, Manuel; Ollitrault, Patrick

2010-11-01

Microsatellite primers were developed from bacterial artificial chromosome (BAC) end sequences of Citrus clementina and their transferability and polymorphism tested in the genus Citrus for future anchorage of physical and genetic maps and comparative interspecific genetic mapping. • Using PAGE and DNA silver staining, 79 primer pairs were selected for their transferability and polymorphism among 526 microsatellites mined in BES. A preliminary diversity study in Citrus was conducted with 18 of them, in C. reticulata, C. maxima, C. medica, C. sinensis, C. aurantium, C. paradisi, C. lemon, C. aurantifolia, and some papedas (wild citrus), using a capillary electrophoresis fragment analyzer. Intra- and interspecific polymorphism was observed, and heterozygous markers were identified for the different genotypes to be used for genetic mapping. • These results indicate the utility of the developed primers for comparative mapping studies and the integration of physical and genetic maps.

Verbal Memory Impairment in Patients with Subsyndromal Bipolar Disorder.

PubMed

Sumiyoshi, Tomiki; Toyomaki, Atsuhito; Kawano, Naoko; Kitajima, Tomoko; Kusumi, Ichiro; Ozaki, Norio; Iwata, Nakao; Sueyoshi, Kazuki; Nakagome, Kazuyuki

2017-01-01

Several domains of cognitive function, including learning memory and executive function, are impaired in mood disorders. Also, the relationship between disturbances of these two cognitive domains has been suggested. In line with the recent initiative to establish a standard measure of cognitive decline in bipolar disorder, the present study was conducted to (1) test the criterion-related validity and test-retest reliability of the California Verbal Learning Test (CVLT)-II Japanese version, and (2) determine if type of word learning tasks (i.e., with or without a category structure) affects severity of verbal memory deficits in patients with subsyndromal bipolar disorder. Thirty-six patients with bipolar disorder with mild symptoms and 42 healthy volunteers participated in the study. We first compared effect sizes for memory deficits in patients among the CVLT-II, Brief Assessment of Cognition in Schizophrenia (BACS), and Hopkins Verbal Memory Tests-Revised (HVLT-R). We next evaluated the correlations between scores of the CVLT-II vs. those of the BACS and HVLT-R. Bipolar patients were re-assessed with the same (standard) or alternate forms of the CVLT-II and HVLT-R 1 month later. Scores on the CVLT-II 1-5 Free Recall and Long-delay Free Recall, as well as the HVLT-R Immediate Recall, but not the BACS List Learning were significantly lower for patients compared to control subjects. The effect sizes for cognitive decline due to the illness were comparable when measured by the CVLT-II and HVLT-R, ranging from 0.5 to 0.6. CVLT-II scores were significantly correlated with those of the HVLT-R and BACS. Test-retest reliability of the CVLT-II was acceptable, and no significant practice effect was observed when the alternate form was used. There was no consistent relationship between mood symptoms and performance on the CVLT-II. These results suggest the CVLT-II Japanese version is able to discriminate between bipolar disorder patients and healthy controls with good sensitivity and validity. Data in this study also indicate that the degree of verbal memory deficits in bipolar disorder may be influenced by memory organizational strategy.

BAC library development, and clone characterization for dormancy-responsive DREB4A, DAM, and FT from leafy spurge (Euphorbia esula L.) identifies differential splicing and conserved promoter motifs

USDA-ARS?s Scientific Manuscript database

We developed two leafy spurge BAC libraries that together represent approximately 5X coverage of the leafy spurge genome. The BAC libraries have an average insert size of approximately 143 kb, and copies of the library and filters for hybridization-based screening are publicly available through the ...

The Association Between HIV Disclosure Status and Perceived Barriers to Care Faced by Women Living with HIV in Latin America, China, Central/Eastern Europe, and Western Europe/Canada.

PubMed

Loutfy, Mona; Johnson, Margaret; Walmsley, Sharon; Samarina, Anna; Vasquez, Patricia; Hao-Lan, He; Madihlaba, Tshepiso; Martinez-Tristani, Marisol; van Wyk, Jean

2016-09-01

Generally, women are less likely than men to disclose their HIV status. This analysis examined the relationship between HIV disclosure and (1) perceived barriers to care and (2) quality of life (QoL) for women with HIV. The ELLA (EpidemioLogical study to investigate the popuLation and disease characteristics, barriers to care, and quAlity of life for women living with HIV) study enrolled HIV-positive women aged ≥18 years. Women completed the 12-item Barriers to Care Scale (BACS) questionnaire. QoL was assessed using the Health Status Assessment. BACS and QoL were stratified by dichotomized HIV disclosure status (to anyone outside the healthcare system). Multilevel logistic regression analysis was used to identify factors associated with disclosure. Of 1945 patients enrolled from Latin America, China, Central/Eastern Europe, and Western Europe/Canada between July 2012 and September 2013, 1929 were included in the analysis (disclosed, n = 1724; nondisclosed, n = 205). Overall, 55% of patients lived with a husband/partner, 53% were employed, and 88% were receiving antiretroviral therapy. Patients who were with a serodiscordant partner were more likely to disclose (p = 0.0003). China had a disproportionately higher percentage of participants who did not disclose at all (nearly 30% vs. <15% for other regions). Mean BACS severity scores for medical/psychological service barriers and most personal resource barriers were significantly lower for the disclosed group compared with the nondisclosed group (p ≤ 0.02 for all). Compared with the disclosed group, the nondisclosed group reported statistically significantly higher (p ≤ 0.03) BACS item severity scores for 8 of the 12 potential barriers to care. The disclosed group reported better QoL. Overall, HIV nondisclosure was associated with more severe barriers to accessing healthcare by women with HIV.

Relationship of impaired-driving enforcement intensity to drinking and driving on the roads.

PubMed

Fell, James C; Waehrer, Geetha; Voas, Robert B; Auld-Owens, Amy; Carr, Katherine; Pell, Karen

2015-01-01

It is principally the area of enforcement that offers the greatest opportunity for reducing alcohol-impaired driving in the near future. How much of a reduction in drinking and driving would be achieved by how much improvement in enforcement intensity? We developed logistic regression models to explore how enforcement intensity (6 different measures) related to the prevalence of weekend nighttime drivers in the 2007 National Roadside Survey who had been drinking (blood alcohol concentration [BAC] ≥ 0.00 g/dl), who had BACs ≥ 0.05 g/dl, and who were driving with an illegal BAC ≥ 0.08 g/dl. Drivers on the roads in our sample of 30 communities who were exposed to fewer than 228 traffic stops per 10,000 population aged 18 and older had 2.4 times the odds of being BAC positive, 3.6 times the odds of driving with a BAC ≥ 0.05, and 3.8 times the odds of driving with a BAC ≥ 0.08 compared to those drivers on the roads in communities with more than 1,275 traffic stops per 10,000 population. Drivers on the roads in communities with fewer than 3.7 driving under the influence (DUI) arrests per 10,000 population had 2.7 times the odds of BAC-positive drivers on the roads compared to communities with the highest intensity of DUI arrest activity (>38 DUI arrests per 10,000 population). The number of traffic stops and DUI arrests per capita were significantly associated with the odds of drinking and driving on the roads in these communities. This might reflect traffic enforcement visibility. The findings in this study may help law enforcement agencies around the country adjust their traffic enforcement intensity to reduce impaired driving in their community. Copyright © 2014 by the Research Society on Alcoholism.

A Blumeria graminisf.sp. hordei BAC library--contig building and microsynteny studies.

PubMed

Pedersen, Carsten; Wu, Boqian; Giese, Henriette

2002-11-01

A bacterial artificial chromosome (BAC) library of Blumeria graminis f.sp. hordei, containing 12,000 clones with an average insert size of 41 kb, was constructed. The library represents about three genome equivalents and BAC-end sequencing showed a high content of repetitive sequences, making contig-building difficult. To identify overlapping clones, several strategies were used: colony hybridisation, PCR screening, fingerprinting techniques and the use of single-copy expressed sequence tags. The latter proved to be the most efficient method for identification of overlapping clones. Two contigs, at or close to avirulence loci, were constructed. Single nucleotide polymorphism (SNP) markers were developed from BAC-end sequences to link the contigs to the genetic maps. Two other BAC contigs were used to study microsynteny between B. graminis and two other ascomycetes, Neurospora crassa and Aspergillus fumigatus. The library provides an invaluable tool for the isolation of avirulence genes from B. graminis and for the study of gene synteny between this fungus and other fungi.

BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple.

PubMed

Han, Yuepeng; Chagné, David; Gasic, Ksenija; Rikkerink, Erik H A; Beever, Jonathan E; Gardiner, Susan E; Korban, Schuyler S

2009-03-01

A genome-wide BAC physical map of the apple, Malus x domestica Borkh., has been recently developed. Here, we report on integrating the physical and genetic maps of the apple using a SNP-based approach in conjunction with bin mapping. Briefly, BAC clones located at ends of BAC contigs were selected, and sequenced at both ends. The BAC end sequences (BESs) were used to identify candidate SNPs. Subsequently, these candidate SNPs were genetically mapped using a bin mapping strategy for the purpose of mapping the physical onto the genetic map. Using this approach, 52 (23%) out of 228 BESs tested were successfully exploited to develop SNPs. These SNPs anchored 51 contigs, spanning approximately 37 Mb in cumulative physical length, onto 14 linkage groups. The reliability of the integration of the physical and genetic maps using this SNP-based strategy is described, and the results confirm the feasibility of this approach to construct an integrated physical and genetic maps for apple.

BAC-MP4 predictions of thermochemistry for the gas-phase tin compounds in the Sn-H-C-Cl system.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allendorf, Mark D.; Melius, Carl F.

2004-09-01

In this work, the BAC-MP4 method is extended for the first time to compounds in the fourth row of the periodic table, resulting in a self-consistent set of thermochemical data for 56 tin-containing molecules in the Sn-H-C-Cl system. The BAC-MP4 method combines ab initio electronic structure calculations with empirical corrections to obtain accurate heats of formation. To obtain electronic energies for tin-containing species, the standard 6-31G(d,p) basis set used in BAC-MP4 calculations is augmented with a relativistic effective core potential to describe the electronic structure of the tin atom. Both stable compounds and radical species are included in this study.more » Trends within homologous series and calculated bond dissociation energies are consistent with previous BAC-MP4 predictions for group 14 compounds and the limited data available from the literature, indicating that the method is performing well for these compounds.« less

Ethanol Forensic Toxicology.

PubMed

Perry, Paul J; Doroudgar, Shadi; Van Dyke, Priscilla

2017-12-01

Ethanol abuse can lead to negative consequences that oftentimes result in criminal charges and civil lawsuits. When an individual is suspected of driving under the influence, law enforcement agents can determine the extent of intoxication by measuring the blood alcohol concentration (BAC) and performing a standardized field sobriety test. The BAC is dependent on rates of absorption, distribution, and elimination, which are influenced mostly by the dose of ethanol ingested and rate of consumption. Other factors contributing to BAC are gender, body mass and composition, food effects, type of alcohol, and chronic alcohol exposure. Because of individual variability in ethanol pharmacology and toxicology, careful extrapolation and interpretation of the BAC is needed, to justify an arrest and assignment of criminal liability. This review provides a summary of the pharmacokinetic properties of ethanol and the clinical effects of acute intoxication as they relate to common forensic questions. Concerns regarding the extrapolation of BAC and the implications of impaired memory caused by alcohol-induced blackouts are discussed. © 2017 American Academy of Psychiatry and the Law.

Effects of introducing an administrative .05% blood alcohol concentration limit on law enforcement patterns and alcohol-related collisions in Canada.

PubMed

Blais, Étienne; Bellavance, François; Marcil, Alexandra; Carnis, Laurent

2015-09-01

Except for Quebec, all Canadian provinces have introduced administrative laws to lower the permitted blood alcohol concentration (BAC) to .05% or .04% for driving-or having the care of-a motor vehicle. Using linear mixed effects models for longitudinal data, this study evaluates the effect of administrative BAC laws on fatal alcohol related crashes and law enforcement patterns in Canada from 1987 to 2010. Results reveal a significant decrease of 3.7% (95% C.I.: 0.9-6.5%) in fatally injured drivers with a BAC level equal or greater than .05% following the introduction of these laws. Reductions were also observed for fatally injured drivers with BAC levels greater that .08% and .15%. The introduction of administrative BAC laws led neither to significant changes in the rate of driving while impaired (DWI) incidents reported by police officers nor in the probability of being charged for DWI under the Criminal Code. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels

PubMed Central

Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L.

2013-01-01

Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail ‘neck’, are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the ‘outer ion’ site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies shows that this site forms a previously unknown determinant of CaV high affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily. PMID:24120938

Bacterial contamination of platelet components not detected by BacT/ALERT®.

PubMed

Abela, M A; Fenning, S; Maguire, K A; Morris, K G

2018-02-01

To investigate the possible causes for false negative results in BacT/ALERT ® 3D Signature System despite bacterial contamination of platelet units. The Northern Ireland Blood Transfusion Service (NIBTS) routinely extends platelet component shelf life to 7 days. Components are sampled and screened for bacterial contamination using an automated microbial detection system, the BacT/ALERT ® 3D Signature System. We report on three platelet components with confirmed bacterial contamination, which represent false negative BacT/ALERT ® results and near-miss serious adverse events. NIBTS protocols for risk reduction of bacterial contamination of platelet components are described. The methodology for bacterial detection using BacT/ALERT ® is outlined. Laboratory tests, relevant patient details and relevant follow-up information are analysed. In all three cases, Staphylococcus aureus was isolated from the platelet residue and confirmed on terminal sub-culture using BacT/ALERT ® . In two cases, S. aureus with similar genetic makeup was isolated from the donors. Risk reduction measures for bacterial contamination of platelet components are not always effective. Automated bacterial culture detection does not eliminate the risk of bacterial contamination. Visual inspection of platelet components prior to release, issue and administration remains an important last line of defence. © 2017 British Blood Transfusion Society.

Characterization of growth and reproduction performance, transgene integration, expression and transmission patterns in transgenic pigs produced by piggyBac transposition-mediated gene transfer

PubMed Central

Zeng, Fang; Li, Zicong; Cai, Gengyuan; Gao, Wenchao; Jiang, Gelong; Liu, Dewu; Urschitz, Johann; Moisyadi, Stefan; Wu, Zhenfang

2016-01-01

Previously we successfully produced a group of EGFP-expressing founder transgenic pigs by a newly developed efficient and simple pig transgenesis method based on cytoplasmic injection of piggyBac plasmids. In this study, we investigated the growth and reproduction performance, and characterized the transgene insertion, transmission and expression patterns in transgenic pigs generated by piggyBac transposition. Results showed that transgene has no injurious effect on the growth and reproduction of transgenic pigs. Multiple copies of monogenic EGFP transgene were inserted at noncoding sequences of host genome, and passed from founder transgenic pigs to their transgenic offspring in segregation or linkage manner. The EGFP transgene was ubiquitously expressed in transgenic pigs, and its expression intensity was associated with transgene copy number but not related to its promoter DNA methylation level. To the best of our knowledge, this is first study that fully described the growth and reproduction performance, transgene insertion, expression and transmission profiles in transgenic pigs produced by piggyBac system. It not only demonstrates that piggyBac transposition-mediated gene transfer is an effective and favourable approach for pig transgenesis, but also provides scientific information for understanding the transgene insertion, expression and transmission patterns in transgenic animals produced by piggyBac transposition. PMID:27565868

Establishing the Brief Assessment of Cognition - Short form.

PubMed

Lam, Max; Wang, Mingyuan; Huang, Wanping; Eng, Goi Khia; Rapisarda, Attilio; Kraus, Michael; Kang, Sim; Keefe, R S E; Lee, Jimmy

2017-10-01

The study aims to identify and validate a parsimonious subset of tests in the commonly used Brief Assessment of Cognition in Schizophrenia (BACS) that allows the evaluation of global cognitive ability. Several permutations of subtests from the BACS were examined to identify the best subset of tests to compose the short form measure. The Brief Assessment of Cognition-Short Form (BAC-SF) was evaluated for convergent validity in healthy and psychiatric samples (N = 3718). Verbal Memory, Digit Sequencing, and Symbol Coding subtests were found to best summarize the variance of composite scores in both Asian and US Norming samples (r = 0.91) indicating that BAC-SF is an appropriate approximation of cognitive deficits. Test re-test reliability of the BAC-SF was adequate (Intraclass Correlation Coefficient (ICC) = 0.73) and showed sufficient separation between healthy controls and schizophrenia (Average Predictive Accuracy = 79.9%; replication = 76.5%). Findings indicate that the BAC-SF an could be used as a cognitive screener for large-scale clinical and epidemiological studies. The short form does not replace the need for comprehensive neuropsychological batteries purposed for detailed neuropsychological and clinical investigation of cognitive function. Further replication of the construct might be necessary in other clinical populations. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genoprotective effect of hyaluronic acid against benzalkonium chloride-induced DNA damage in human corneal epithelial cells

PubMed Central

Wu, Han; Zhang, Huina; Wang, Changjun; Wu, Yihua; Xie, Jiajun; Jin, Xiuming; Yang, Jun

2011-01-01

Purpose The aim of this study was to investigate hyaluronic acid (HA) protection on cultured human corneal epithelial cells (HCEs) against benzalkonium chloride (BAC)-induced DNA damage and intracellular reactive oxygen species (ROS) increase. Methods Cells were incubated with different concentrations of BAC with or without the presence of 0.2% HA for 30 min. DNA damage to HCEs was examined by alkaline comet assay and by immunofluorescence microscopic detection of the phosphorylated form of histone variant H2AX (γH2AX) foci. ROS production was assessed by the fluorescent probe, 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA). Cell apoptosis was determined with annexin V staining by flow cytometry. Results HA significantly reduced BAC-induced DNA damage as indicated by the tail length (TL) and tail moment (TM) of alkaline comet assay and by γH2AX foci formation, respectively. Moreover, HA significantly decreased BAC-induced ROS increase and cell apoptosis. However, exposure to HA alone did not produce any significant change in DNA damage, ROS generation, or cell apoptosis. Conclusions BAC could induce DNA damage and cell apoptosis in HCEs, probably through increasing oxidative stress. Furthermore, HA was an effective protective agent that had antioxidant properties and could decrease DNA damage and cell apoptosis induced by BAC. PMID:22219631

DNA modification and functional delivery into human cells using Escherichia coli DH10B

PubMed Central

Narayanan, Kumaran; Warburton, Peter E.

2003-01-01

The availability of almost the complete human genome as cloned BAC libraries represents a valuable resource for functional genomic analysis, which, however, has been somewhat limited by the ability to modify and transfer this DNA into mammalian cells intact. Here we report a novel comprehensive Escherichia coli-based vector system for the modification, propagation and delivery of large human genomic BAC clones into mammalian cells. The GET recombination inducible homologous recombination system was used in the BAC host strain E.coli DH10B to precisely insert an EGFPneo cassette into the vector portion of a ∼200 kb human BAC clone, providing a relatively simple method to directly convert available BAC clones into suitable vectors for mammalian cells. GET recombination was also used for the targeted deletion of the asd gene from the E.coli chromosome, resulting in defective cell wall synthesis and diaminopimelic acid auxotrophy. Transfer of the Yersinia pseudotuberculosis invasin gene into E.coli DH10B asd– rendered it competent to invade HeLa cells and deliver DNA, as judged by transient expression of green fluorescent protein and stable neomycin-resistant colonies. The efficiency of DNA transfer and survival of HeLa cells has been optimized for incubation time and multiplicity of infection of invasive E.coli with HeLa cells. This combination of E.coli-based homologous recombination and invasion technologies using BAC host strain E.coli DH10B will greatly improve the utility of the available BAC libraries from the human and other genomes for gene expression and functional genomic studies. PMID:12711696

A mouse dry eye model induced by topical administration of benzalkonium chloride.

PubMed

Lin, Zhirong; Liu, Xiaochen; Zhou, Tong; Wang, Yihui; Bai, Li; He, Hui; Liu, Zuguo

2011-01-25

To develop a dry eye model of mouse induced by topical administration of benzalkonium chloride (BAC) and investigate the possible mechanisms. BAC at concentration of 0.2% was applied to the mouse ocular surface for 7 days. Phenol red thread tear test, tear break-up time (BUT) test, corneal inflammatory index scoring, fluorescein and rose bengal test were performed to evaluate the toxic effects of BAC on the ocular surface. Global specimens were collected on day (D) 7 and labeled with a series of antibodies including cytokeratin 10 (K10) and mucin 5AC (MUC5AC). Apoptosis of ocular surface epithelium was evaluated by in situ terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. Histologic analysis and transmission electron microscopy (TEM) were performed on D7. BAC at a concentration of 0.2% successfully induced a dry eye condition with decreased tear volume and BUTs, increased corneal fluorescein and rose bengal scores. The Inflammatory index was increased in accompaniment with higher tumor necrosis factor-α (TNF-α) expression and more inflammatory infiltration in the cornea. Immunolabeling revealed positive K10 expression in BAC-treated corneal epithelium and fewer MUC5AC-positive cells in the BAC-treated conjunctival fornix. TUNEL assay showed more apoptotic cells in the corneal basal epithelium. TEM showed that the size and intervals of the microvillis were both reduced in the corneal epithelium. Topical administration of 0.2% BAC in mouse induces changes resembling that of dry eye syndrome in humans, and thus, represents a novel model of dry eye.

The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

PubMed Central

Bonet, Julio; Girona, Elena Lopez; Sargent, Daniel J; Muñoz-Torres, Monica C; Monfort, Amparo; Abbott, Albert G; Arús, Pere; Simpson, David W; Davik, Jahn

2009-01-01

Background The cultivated strawberry Fragaria ×ananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library. Methods A BAC library, consisting of 18,432 clones was constructed from Fragaria vesca f. semperflorens accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid Fragaria reference map (FV×FN). Findings Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid Fragaria FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid Fragaria genome, which is in accordance with the estimate of library coverage based on average insert size. Conclusion This BAC library will be used for the construction of a physical map for F. vesca and the superpools will permit physical anchoring of molecular markers using PCR. PMID:19772672

A mouse dry eye model induced by topical administration of benzalkonium chloride

PubMed Central

Lin, Zhirong; Liu, Xiaochen; Zhou, Tong; Wang, Yihui; Bai, Li; He, Hui

2011-01-01

Purpose To develop a dry eye model of mouse induced by topical administration of benzalkonium chloride (BAC) and investigate the possible mechanisms. Methods BAC at concentration of 0.2% was applied to the mouse ocular surface for 7 days. Phenol red thread tear test, tear break-up time (BUT) test, corneal inflammatory index scoring, fluorescein and rose bengal test were performed to evaluate the toxic effects of BAC on the ocular surface. Global specimens were collected on day (D) 7 and labeled with a series of antibodies including cytokeratin 10 (K10) and mucin 5AC (MUC5AC). Apoptosis of ocular surface epithelium was evaluated by in situ terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. Histologic analysis and transmission electron microscopy (TEM) were performed on D7. Results BAC at a concentration of 0.2% successfully induced a dry eye condition with decreased tear volume and BUTs, increased corneal fluorescein and rose bengal scores. The Inflammatory index was increased in accompanyment with higher tumor necrosis factor-α (TNF-α) expression and more inflammatory infiltration in the cornea. Immunolabeling revealed positive K10 expression in BAC-treated corneal epithelium and fewer MUC5AC-positive cells in the BAC-treated conjunctival fornix. TUNEL assay showed more apoptotic cells in the corneal basal epithelium. TEM showed that the size and intervals of the microvillis were both reduced in the corneal epithelium. Conclusions Topical administration of 0.2% BAC in mouse induces changes resembling that of dry eye syndrome in humans, and thus, represents a novel model of dry eye. PMID:21283525

How Should Remote Clinical Monitoring Be Used to Treat Alcohol Use Disorders?: Initial Findings From an Expert Round Table Discussion.

PubMed

Gordon, Alan; Jaffe, Adi; McLellan, A Thomas; Richardson, Gary; Skipper, Gregory; Sucher, Michel; Tirado, Carlos F; Urschel, Harold C

Scientific evidence combined with new health insurance coverage now enable a chronic illness management approach to the treatment of alcohol use disorders (AUDs), including regular monitoring of blood alcohol content (BAC), as a useful indicator of disease control. Recent technical advances now permit many different types of remote, real-time monitoring of BAC. However, there is no body of research to empirically guide clinicians in how to maximize the clinical potential of remote BAC monitoring.As an initial step in guiding and supporting such research, the manufacturer of one remote BAC monitoring system sponsored a group of experienced clinicians and clinical researchers to discuss 8 issues that generally affect remote, clinical BAC monitoring of "adults in outpatient AUD treatment."The expert panel unanimously agreed that remote BAC monitoring for at least 12 months during and after the outpatient treatment of AUD was a clinically viable deterrent to relapse. There was also consensus that positive test results (ie, recent alcohol use) should lead to intensified care and monitoring. However, there was no agreement on specific types of clinical intensification after a positive test. The panel agreed that sharing positive and negative test results with members of the patient support group was helpful in reinforcing abstinence, yet they noted many practical issues regarding information sharing that remain concerning. Significant differences within the panel on several important clinical issues underline the need for more clinical and implementation research to produce empirically-supported guidelines for the use of remote BAC monitoring in AUD treatment.

How Should Remote Clinical Monitoring Be Used to Treat Alcohol Use Disorders?: Initial Findings From an Expert Round Table Discussion

PubMed Central

Gordon, Alan; Jaffe, Adi; McLellan, A. Thomas; Richardson, Gary; Skipper, Gregory; Sucher, Michel; Tirado, Carlos F.; Urschel, Harold C.

2017-01-01

Scientific evidence combined with new health insurance coverage now enable a chronic illness management approach to the treatment of alcohol use disorders (AUDs), including regular monitoring of blood alcohol content (BAC), as a useful indicator of disease control. Recent technical advances now permit many different types of remote, real-time monitoring of BAC. However, there is no body of research to empirically guide clinicians in how to maximize the clinical potential of remote BAC monitoring. As an initial step in guiding and supporting such research, the manufacturer of one remote BAC monitoring system sponsored a group of experienced clinicians and clinical researchers to discuss 8 issues that generally affect remote, clinical BAC monitoring of “adults in outpatient AUD treatment.” The expert panel unanimously agreed that remote BAC monitoring for at least 12 months during and after the outpatient treatment of AUD was a clinically viable deterrent to relapse. There was also consensus that positive test results (ie, recent alcohol use) should lead to intensified care and monitoring. However, there was no agreement on specific types of clinical intensification after a positive test. The panel agreed that sharing positive and negative test results with members of the patient support group was helpful in reinforcing abstinence, yet they noted many practical issues regarding information sharing that remain concerning. Significant differences within the panel on several important clinical issues underline the need for more clinical and implementation research to produce empirically-supported guidelines for the use of remote BAC monitoring in AUD treatment. PMID:28157829

[Construction of a recombinant HVT virus expressing the HA gene of avian influenza virus H5N1 via Rde/ET recombination system].

PubMed

Lan, Desong; Shi, Xingming; Wang, Yunfeng; Liu, Changjun; Wang, Mei; Cui, Hongyu; Tian, Guobin; Li, Jisong; Tong, Guangzhi

2009-01-01

In recent years,manipulation of large herpesvirus genomes has been facilitated by using bacterial artificial chromosome (BAC) vectors. We have previously reported the construction of the BAC clones (HVT BACs) of herpesvirus of turkey (HVT). With these BAC clones in hand,we manipulated the genome of HVT by utilizing Red/ET recombination system, and developed a biologically safe live vaccine based on the HVT BACs. In this two-step approach, we first transformed the plasmid pRedET into the DH10B competent cells that carried the HVT BACs,and added inducer L-arabinose into the cells. We prepared the cells into competent cells and electroporated the linear rpsL-neo counter-selection/selection cassette flanked by the 50 bp long homology arms into the cells. So the functional cassette was inserted into the U(S)2 locus. Only colonies carrying the modified BAC would survive Kanamycin selection on the agar plates. The successful integration of the rpsL-neo cassette was monitored by PCR and Streptomycin selection, for the insertion of rpsL-neo cassette cells will become Streptomycin sensitive. Secondly, in the same way, we replaced the rpsL-neo cassette with the hemagglutinin (HA) gene of (HPAIV) A/Goose/ Guangdong/1/96(H5N1) flanked by the same homology arms. Only colonies which lost the rpsL-neo cassette will grow on Streptomycin containing plates. Finally, we obtained many colonies of which the HA gene of the AIV was inserted into the U(S)2 locus to be modified of HVT. And we reconstituted one recombinant virus from transfecting one of these BAC clones DNA into chick embryo fibroblasts (CEFs). We achieved one rescued recombinant virus which designated as rHVT-HA3. The H5 subtype HA gene expression in this recombinant virus rHVT-HA3 was confirmed by immunofluorescence assay.

Development of diagnostic prediction tools for bacteraemia caused by third-generation cephalosporin-resistant enterobacteria in suspected bacterial infections: a nested case-control study.

PubMed

Rottier, W C; van Werkhoven, C H; Bamberg, Y R P; Dorigo-Zetsma, J W; van de Garde, E M; van Hees, B C; Kluytmans, J A J W; Kuck, E M; van der Linden, P D; Prins, J M; Thijsen, S F T; Verbon, A; Vlaminckx, B J M; Ammerlaan, H S M; Bonten, M J M

2018-03-23

Current guidelines for the empirical antibiotic treatment predict the presence of third-generation cephalosporin-resistant enterobacterial bacteraemia (3GCR-E-Bac) in case of infection only poorly, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems which can better predict the presence of 3GCR-E-Bac. A retrospective nested case-control study was performed that included patients ≥18 years of age from eight Dutch hospitals in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GCR-E-Bac was matched to four control infection episodes within the same hospital, based on blood-culture date and onset location (community or hospital). Starting from 32 commonly described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GCR-E-Bac. 3GCR-E-Bac occurred in 90 of 22 506 (0.4%) community-onset infections and in 82 of 8110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes. The derived community-onset and hospital-onset scoring systems consisted of six and nine predictors, respectively. With selected score cut-offs, the models identified 3GCR-E-Bac with sensitivity equal to existing guidelines (community-onset: 54.3%; hospital-onset: 81.5%). However, they reduced the proportion of patients classified as at risk for 3GCR-E-Bac (i.e. eligible for empirical carbapenem therapy) with 40% (95%CI 21-56%) and 49% (95%CI 39-58%) in, respectively, community-onset and hospital-onset infections. These prediction scores for 3GCR-E-Bac, specifically geared towards the initiation of empirical antibiotic treatment, may improve the balance between inappropriate antibiotics and carbapenem overuse. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Effects of acute alcohol tolerance on perceptions of danger and willingness to drive after drinking.

PubMed

Amlung, Michael T; Morris, David H; McCarthy, Denis M

2014-11-01

Drinking and driving is associated with elevated rates of motor vehicle accidents and fatalities. Previous research suggests that alcohol impairs judgments about the dangers of risky behaviors; however, how alcohol affects driving-related judgments is less clear. Impairments have also been shown to differ across limbs of the blood alcohol concentration (BAC) curve, which is known as acute tolerance. The objectives of this study were to examine whether perceptions about the dangerousness of driving after drinking and willingness to drive differed across the ascending and descending limbs of the BAC curve and to test whether reductions in perceived danger were associated with willingness to drive on the descending limb. Fifty-six participants were randomly assigned to receive either a moderate dose of alcohol (peak BAC = 0.10 g%) or placebo. We assessed perceived dangerousness and willingness to drive at matched BACs (~0.067-0.068 g%) on the ascending and descending limbs. Both perceived danger and willingness to drive showed acute tolerance in the alcohol group. Participants judged driving to be significantly less dangerous and were more willing to drive on the descending limb compared to the ascending limb. The magnitude of change in perceived danger significantly predicted willingness to drive on the descending limb. Decreased impairment associated with acute tolerance may lead individuals to underestimate the dangerousness of driving after drinking and in turn make poor decisions regarding driving. This study further emphasizes the descending limb as a period of increased risk and offers support for enhancing prevention efforts by targeting drivers at declining BAC levels.

Bayesian effect estimation accounting for adjustment uncertainty.

PubMed

Wang, Chi; Parmigiani, Giovanni; Dominici, Francesca

2012-09-01

Model-based estimation of the effect of an exposure on an outcome is generally sensitive to the choice of which confounding factors are included in the model. We propose a new approach, which we call Bayesian adjustment for confounding (BAC), to estimate the effect of an exposure of interest on the outcome, while accounting for the uncertainty in the choice of confounders. Our approach is based on specifying two models: (1) the outcome as a function of the exposure and the potential confounders (the outcome model); and (2) the exposure as a function of the potential confounders (the exposure model). We consider Bayesian variable selection on both models and link the two by introducing a dependence parameter, ω, denoting the prior odds of including a predictor in the outcome model, given that the same predictor is in the exposure model. In the absence of dependence (ω= 1), BAC reduces to traditional Bayesian model averaging (BMA). In simulation studies, we show that BAC, with ω > 1, estimates the exposure effect with smaller bias than traditional BMA, and improved coverage. We, then, compare BAC, a recent approach of Crainiceanu, Dominici, and Parmigiani (2008, Biometrika 95, 635-651), and traditional BMA in a time series data set of hospital admissions, air pollution levels, and weather variables in Nassau, NY for the period 1999-2005. Using each approach, we estimate the short-term effects of on emergency admissions for cardiovascular diseases, accounting for confounding. This application illustrates the potentially significant pitfalls of misusing variable selection methods in the context of adjustment uncertainty. © 2012, The International Biometric Society.

Environmental risk assessment and consequences of municipal solid waste disposal.

PubMed

Vaverková, Magdalena Daria; Elbl, Jakub; Radziemska, Maja; Adamcová, Dana; Kintl, Antonín; Baláková, Ludmila; Bartoň, Stanislav; Hladký, Jan; Kynický, Jindřich; Brtnický, Martin

2018-06-04

Effective and efficient assessments of the site conditions are required for the sustainable management of landfills. In this study we propose an evaluation method to determine the degree of environmental contamination by the contest of heavy metals (HM) concentrations in soil and plants (Tanacetum vulgare L., Carduus L., Plantago major L.). We compared HM concentrations in the soil, leaves, stem and roots of those native plants. Content of HM in samples was at the same level in all localities, except content of Zn. These values confirm that the area is not naturally burdened by increased HM content in the soil, and also that the deposited municipal waste or the material used for reclamation and composting does not contain risk elements. The content of selected HM was monitored in plants naturally occurring in the area of interest. We can state that the content of individual HM was in the plant biomass at the same level. The measured values confirmed that the largest number of HM was in roots, then in stem and the least in leaves. In addition, specific indexes were determined: BAC, TF, CF, PLI and I geo . The BAC values confirmed that the individual plants had the ability to accumulate Pb and Cd (BAC> 2) but were limited to bind Mn and Zn (BAC <1). TF values confirmed that plants had a different ability to transport HM from roots to aboveground biomass. Potential soil contamination was detected using CF, PLI and I geo indexes but contamination by HM was not confirmed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Perception of traffic accident risk and decision to drive under light alcohol consumption--a double-blind experimental study.

PubMed

Frick, U; Rehm, J; Knoll, A; Reifinger, M; Hasford, J

2000-01-01

Public traffic safety campaigns in Germany have focussed on the changing risk perception of young drivers. While there is some consensus that perceptions of risk affect driving, less is understood about the relationship and interaction of alcohol consumption and risk perception on the decision to drive. We examined the influence of light alcohol consumption on risk perception and decision to drive, and the interaction of alcohol consumption and cognitive feedback on the handicapping effect of alcohol on risk perception and decision to drive. In a double-blind block-randomized experimental study of 104 young drivers between 19 and 24 years of age, with two experimentally manipulated independent factors of alcohol consumption (three levels: 0% BAC, 0.015% BAC, 0.03% BAC) and feedback (positive or negative), we assessed three dependent variables: perception of traffic accident risk, subjective judgement about driving-relevant cognitive performance, decision to drive a car. Analyses of variance and covariance were used to analyze differences between levels of experimental factors. We found that persons with 0.015 BAC performed better than persons in both other alcohol conditions on the standardized risk perception task. Perceived handicap of driving was significantly more pronounced for negative feedback compared to positive feedback with no influence of the level of alcohol consumption. No significant influence on decision to drive was found of either level of alcohol consumption, feedback or sex. Decision to drive in young drivers could not be influenced by feedback or light consumption. Public health approaches have to find better determining factors.

Driving Performance Under Alcohol in Simulated Representative Driving Tasks

PubMed Central

Kenntner-Mabiala, Ramona; Kaussner, Yvonne; Jagiellowicz-Kaufmann, Monika; Hoffmann, Sonja; Krüger, Hans-Peter

2015-01-01

Abstract Comparing drug-induced driving impairments with the effects of benchmark blood alcohol concentrations (BACs) is an approved approach to determine the clinical relevance of findings for traffic safety. The present study aimed to collect alcohol calibration data to validate findings of clinical trials that were derived from a representative test course in a dynamic driving simulator. The driving performance of 24 healthy volunteers under placebo and with 0.05% and 0.08% BACs was measured in a double-blind, randomized, crossover design. Trained investigators assessed the subjects’ driving performance and registered their driving errors. Various driving parameters that were recorded during the simulation were also analyzed. Generally, the participants performed worse on the test course (P < 0.05 for the investigators’ assessment) under the influence of alcohol. Consistent with the relevant literature, lane-keeping performance parameters were sensitive to the investigated BACs. There were significant differences between the alcohol and placebo conditions in most of the parameters analyzed. However, the total number of errors was the only parameter discriminating significantly between all three BAC conditions. In conclusion, data show that the present experimental setup is suitable for future psychopharmacological research. Thereby, for each drug to be investigated, we recommend to assess a profile of various parameters that address different levels of driving. On the basis of this performance profile, the total number of driving errors is recommended as the primary endpoint. However, this overall endpoint should be completed by a specifically sensitive parameter that is chosen depending on the effect known to be induced by the tested drug. PMID:25689289

Polygenic risk for schizophrenia and measured domains of cognition in individuals with psychosis and controls.

PubMed

Shafee, Rebecca; Nanda, Pranav; Padmanabhan, Jaya L; Tandon, Neeraj; Alliey-Rodriguez, Ney; Kalapurakkel, Sreeja; Weiner, Daniel J; Gur, Raquel E; Keefe, Richard S E; Hill, Scot K; Bishop, Jeffrey R; Clementz, Brett A; Tamminga, Carol A; Gershon, Elliot S; Pearlson, Godfrey D; Keshavan, Matcheri S; Sweeney, John A; McCarroll, Steven A; Robinson, Elise B

2018-04-12

Psychotic disorders including schizophrenia are commonly accompanied by cognitive deficits. Recent studies have reported negative genetic correlations between schizophrenia and indicators of cognitive ability such as general intelligence and processing speed. Here we compare the effect of polygenetic risk for schizophrenia (PRS SCZ ) on measures that differ in their relationships with psychosis onset: a measure of current cognitive abilities (the Brief Assessment of Cognition in Schizophrenia, BACS) that is greatly reduced in psychotic disorder patients, a measure of premorbid intelligence that is minimally affected by psychosis onset (the Wide-Range Achievement Test, WRAT); and educational attainment (EY), which covaries with both BACS and WRAT. Using genome-wide single nucleotide polymorphism (SNP) data from 314 psychotic and 423 healthy research participants in the Bipolar-Schizophrenia Network for Intermediate Phenotypes (B-SNIP) Consortium, we investigated the association of PRS SCZ with BACS, WRAT, and EY. Among apparently healthy individuals, greater genetic risk for schizophrenia (PRS SCZ ) was significantly associated with lower BACS scores (r = -0.17, p = 6.6 × 10 -4 at P T  = 1 × 10 -4 ), but not with WRAT or EY. Among individuals with psychosis, PRS SCZ did not associate with variations in any of these three phenotypes. We further investigated the association between PRS SCZ and WRAT in more than 4500 healthy subjects from the Philadelphia Neurodevelopmental Cohort. The association was again null (p > 0.3, N = 4511), suggesting that different cognitive phenotypes vary in their etiologic relationship with schizophrenia.

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

Moderate sleep deprivation produces impairments in cognitive and motor performance equivalent to legally prescribed levels of alcohol intoxication

PubMed Central

Williamson, A; Feyer, A.

2000-01-01

OBJECTIVES—To compare the relative effects on performance of sleep deprivation and alcohol.
METHODS—Performance effects were studied in the same subjects over a period of 28 hours of sleep deprivation and after measured doses of alcohol up to about 0.1% blood alcohol concentration (BAC). There were 39 subjects, 30 employees from the transport industry and nine from the army.
RESULTS—After 17-19 hours without sleep, corresponding to 2230 and 0100, performance on some tests was equivalent or worse than that at a BAC of 0.05%. Response speeds were up to 50% slower for some tests and accuracy measures were significantly poorer than at this level of alcohol. After longer periods without sleep, performance reached levels equivalent to the maximum alcohol dose given to subjects (BAC of 0.1%).
CONCLUSIONS—These findings reinforce the evidence that the fatigue of sleep deprivation is an important factor likely to compromise performance of speed and accuracy of the kind needed for safety on the road and in other industrial settings.


Keywords: sleep deprivation; performance; alcohol PMID:10984335

Energy drinks and alcohol: links to alcohol behaviors and consequences across 56 days.

PubMed

Patrick, Megan E; Maggs, Jennifer L

2014-04-01

To examine short-term consequences associated with consuming alcohol and energy drinks compared with consuming alcohol without energy drinks. A longitudinal measurement-burst design (14-day bursts of daily surveys in four consecutive college semesters) captured both within-person variation across occasions and between-person differences across individuals. The analytic sample of late adolescent alcohol users included 4,203 days with alcohol use across up to four semesters per person from 508 college students. Adding energy drink use to a given day with alcohol use was associated with an increase in number of alcoholic drinks, a trend toward more hours spent drinking, elevated estimated blood alcohol content (eBAC), a greater likelihood of subjective intoxication, and more negative consequences of drinking that day. After controlling for eBAC, energy drink use no longer predicted subjective intoxication but was still associated with a greater number of negative consequences. The consumption of energy drinks may lead to increases in alcohol consumption and, after controlling for eBAC, negative consequences. Use of energy drinks plus alcohol represents an emerging threat to public health. Copyright © 2014 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Fine mapping suggests that the goat Polled Intersex Syndrome and the human Blepharophimosis Ptosis Epicanthus Syndrome map to a 100-kb homologous region.

PubMed

Schibler, L; Cribiu, E P; Oustry-Vaiman, A; Furet, J P; Vaiman, D

2000-03-01

To clone the goat Polled Intersex Syndrome (PIS) gene(s), a chromosome walk was performed from six entry points at 1q43. This enabled 91 BACs to be recovered from a recently constructed goat BAC library. Six BAC contigs of goat chromosome 1q43 (ICC1-ICC6) were thus constructed covering altogether 4.5 Mb. A total of 37 microsatellite sequences were isolated from this 4.5-Mb region (16 in this study), of which 33 were genotyped and mapped. ICC3 (1500 kb) was shown by genetic analysis to encompass the PIS locus in a approximately 400-kb interval without recombinants detected in the resource families (293 informative meioses). A strong linkage disequilibrium was detected among unrelated animals with the two central markers of the region, suggesting a probable location for PIS in approximately 100 kb. High-resolution comparative mapping with human data shows that this DNA segment is the homolog of the human region associated with Blepharophimosis Ptosis Epicanthus inversus Syndrome (BPES) gene located in 3q23. This finding suggests that homologous gene(s) could be responsible for the pathologies observed in humans and goats.

Benzalkonium Chloride: A Bronchoconstricting Preservative in Continuous Albuterol Nebulizer Solutions.

PubMed

Prabhakaran, Sreekala; Abu-Hasan, Mutasim; Hendeles, Leslie

2017-05-01

For convenience, many pediatric hospitals are preparing solutions for continuous nebulized albuterol using the 0.5% 20-ml multidose albuterol dropper bottle. This product contains benzalkonium chloride (BAC) that, by itself, produces bronchospasm that is dose dependent and cumulative. The bronchoconstrictive effects of BAC are greater in patients with more severe airway obstruction and increased airway responsiveness. Use of BAC-containing albuterol during severe acute asthma exacerbations may antagonize the bronchodilator response to albuterol, prolong treatment, and increase the risk of albuterol-related systemic adverse effects. Such a deleterious effect of BAC is difficult to detect because some patients improve slowly or may even worsen during treatment. We recommend that only preservative-free albuterol products be used. © 2017 Pharmacotherapy Publications, Inc.

[Jejunal myenteric denervation induced by benzalkonium chloride].

PubMed

Ramalho, F S; Santos, G C; Ramalho, L N; Kajiwara, J K; Zucoloto, S

1994-01-01

The effects of benzalkonium chloride (BAC) on the number of myenteric neurons, muscle thickness and external perimeter after acute (until 10 days after BAC application) and chronic (30 and 60 days after BAC application) denervation of the proximal jejunum were determined in rats. There was a significant reduction in the number of myenteric neurons of all segments treated with BAC. The extent of denervation varied along the time, and it was reduced in the denervated segments of the chronic group in comparison with the acute group. This may be due to the neuroplasticity phenomenon appearing during the chronic phase. Myenteric denervation increased the thickness of the propria muscle layer, especially in the longitudinal muscle layer, suggesting a higher sensitivity of this layer to myenteric denervation.

Integrating field methodology and web-based data collection to assess the reliability of the Alcohol Use Disorders Identification Test (AUDIT).

PubMed

Celio, Mark A; Vetter-O'Hagen, Courtney S; Lisman, Stephen A; Johansen, Gerard E; Spear, Linda P

2011-12-01

Field methodologies offer a unique opportunity to collect ecologically valid data on alcohol use and its associated problems within natural drinking environments. However, limitations in follow-up data collection methods have left unanswered questions regarding the psychometric properties of field-based measures. The aim of the current study is to evaluate the reliability of self-report data collected in a naturally occurring environment - as indexed by the Alcohol Use Disorders Identification Test (AUDIT) - compared to self-report data obtained through an innovative web-based follow-up procedure. Individuals recruited outside of bars (N=170; mean age=21; range 18-32) provided a BAC sample and completed a self-administered survey packet that included the AUDIT. BAC feedback was provided anonymously through a dedicated web page. Upon sign in, follow-up participants (n=89; 52%) were again asked to complete the AUDIT before receiving their BAC feedback. Reliability analyses demonstrated that AUDIT scores - both continuous and dichotomized at the standard cut-point - were stable across field- and web-based administrations. These results suggest that self-report data obtained from acutely intoxicated individuals in naturally occurring environments are reliable when compared to web-based data obtained after a brief follow-up interval. Furthermore, the results demonstrate the feasibility, utility, and potential of integrating field methods and web-based data collection procedures. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Emotional Intelligence deficits in schizophrenia: The impact of non-social cognition.

PubMed

Frajo-Apor, Beatrice; Pardeller, Silvia; Kemmler, Georg; Welte, Anna-Sophia; Hofer, Alex

2016-04-01

Previous studies using the Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT) revealed significant performance deficits across all areas of Emotional Intelligence (EI) in schizophrenia patients compared to healthy controls. However, none of these studies has investigated a potential influence of non-social cognition on these findings. 56 schizophrenia outpatients and 84 control subjects were investigated using the MSCEIT and the Brief Assessment of Cognition in Schizophrenia (BACS). Analyses of covariance were performed with adjustment for the BACS composite score and education. To investigate this issue in more detail, a mediation analysis was conducted. Patients showed significantly lower EI and non-social cognition levels compared to healthy controls. After adjustment for BACS composite score and education, only the group difference in the "managing emotions" branch and thus in the "strategic" EI part of the MSCEIT remained statistically significant, whereas for all other MSCEIT branches (perceiving, using, understanding emotions) statistical significance was lost. The mediation analysis revealed that the difference between schizophrenia patients and controls regarding the MSCEIT total score was almost fully attributable to the mediating effect of non-social cognition. Our findings suggest that in schizophrenia patients EI is largely influenced by non-social cognitive functioning. Only the "managing emotions" branch was found to be independent of non-social cognition. Consequently, non-social cognitive performance was mainly responsible for the observed differences in EI between schizophrenia patients and controls. This has to be taken into account when interpreting MSCEIT data in this population. Copyright © 2016 Elsevier B.V. All rights reserved.

Single- and dual-task performance during on-the-road driving at a low and moderate dose of alcohol: A comparison between young novice and more experienced drivers.

PubMed

Jongen, Stefan; van der Sluiszen, Nick N J J M; Brown, Dennis; Vuurman, Eric F P M

2018-05-01

Driving experience and alcohol are two factors associated with a higher risk of crash involvement in young novice drivers. Driving a car is a complex task involving multiple tasks leading to dividing attention. The aim of this study was to compare the single and combined effects of a low and moderate dose of alcohol on single- and dual-task performance between young novice and more experienced young drivers during actual driving. Nine healthy novice drivers were compared with 9 more experienced drivers in a three-way, placebo-controlled, cross-over study design. Driving performance was measured in actual traffic, with standard deviation of lateral position as the primary outcome variable. Secondary task performance was measured with an auditory word learning test during driving. Results showed that standard deviation of lateral position increased dose-dependently at a blood alcohol concentration (BAC) of 0.2 and 0.5 g/L in both novice and experienced drivers. Secondary task performance was impaired in both groups at a BAC of 0.5 g/L. Furthermore, it was found that driving performance in novice drivers was already impaired at a BAC of 0.2 g/L during dual-task performance. The findings suggest that young inexperienced drivers are especially vulnerable to increased mental load while under the influence of alcohol. © 2018 The Authors Human Psychopharmacology: Clinical and Experimental Published by John Wiley & Sons Ltd.

Discovery of the youngest sex chromosomes reveals first case of convergent co-option of ancestral autosomes in turtles.

PubMed

Montiel, E E; Badenhorst, D; Tamplin, J; Burke, R L; Valenzuela, N

2017-02-01

Most turtle species possess temperature-dependent sex determination (TSD), but genotypic sex determination (GSD) has evolved multiple times independently from the TSD ancestral condition. GSD in animals typically involves sex chromosomes, yet the sex chromosome system of only 9 out of 18 known GSD turtles has been characterized. Here, we combine comparative genome hybridization (CGH) and BAC clone fluorescent in situ hybridization (BAC FISH) to identify a macro-chromosome XX/XY system in the GSD wood turtle Glyptemys insculpta (GIN), the youngest known sex chromosomes in chelonians (8-20 My old). Comparative analyses show that GIN-X/Y is homologous to chromosome 4 of Chrysemys picta (CPI) painted turtles, chromosome 5 of Gallus gallus chicken, and thus to the X/Y sex chromosomes of Siebenrockiella crassicollis black marsh turtles. We tentatively assign the gene content of the mapped BACs from CPI chromosome 4 (CPI-4) to GIN-X/Y. Chromosomal rearrangements were detected in G. insculpta sex chromosome pair that co-localize with the male-specific region of GIN-Y and encompass a gene involved in sexual development (Wt1-a putative master gene in TSD turtles). Such inversions may have mediated the divergence of G. insculpta sex chromosome pair and facilitated GSD evolution in this turtle. Our results illuminate the structure, origin, and evolution of sex chromosomes in G. insculpta and reveal the first case of convergent co-option of an autosomal pair as sex chromosomes within chelonians.

Alcohol and suicide in the Nenets Autonomous Okrug and Arkhangelsk Oblast, Russia

PubMed Central

Sumarokov, Yury A.; Brenn, Tormod; Kudryavtsev, Alexander V.; Sidorenkov, Oleg; Nilssen, Odd

2016-01-01

Background High suicide rates in the Russian North are coupled with high alcohol consumption in the described populations. Objective To investigate the potential role of alcohol consumption on suicides in the Nenets Autonomous Okrug (NAO) in 2002–2012 and to compare this information with corresponding data from the neighboring Arkhangelsk Oblast (AO). Design Retrospective population-based mortality study. Methods Data from autopsy reports were used to identify 252 cases of suicide in the NAO and 1,198 cases in the AO in the period 2002–2012. Postmortem blood alcohol content (BAC) was available for 228 cases in the NAO and 1,185 cases in the AO. BAC as well as other selected variables were compared between the NAO and the AO among women and men, different age groups, ethnic groups, and selected variables of suicide. Results Alcohol was present in the blood of 74.1% of male and 82.9% of female suicide cases in the NAO, which was significantly higher than the proportions found in the AO (59.3% of male and 46.6% female cases). BAC<1.0‰ and between 2.0 and 3.0‰ were more frequently found among suicide cases in the NAO than those in the AO. Conclusions Our findings specify that alcohol drinking may be an essential risk factor for suicide in the NAO, and that this factor may be of greater importance in the indigenous population of the NAO than among Russians in the AO. PMID:27452190

Baicalein alters PI3K/Akt/GSK3β signaling pathway in rats with diabetes-associated cognitive deficits

PubMed Central

Qi, Zhonghua; Xu, Yinghui; Liang, Zhanhua; Li, Sheng; Wang, Jie; Wei, Yi; Dong, Bin

2015-01-01

Our present investigation focused on assessing the neuroprotective potential of baicalein (BAC) against diabetes-associated cognitive deficit (DACD) using a diabetic model and further figure out the potential molecular mechanisms. Diabetic rat model was established by streptozotocin (STZ). Vehicle or BAC by the doses of 2 and 4 mg/kg was intraperitoneally injected once a day for seven consecutive weeks. Memory function was evaluated by Morris water maze test and avoidance passive test. The activities of acetylcholinesterase (AChE), choline acetylase (ChAT), caspase-9 and caspase-3 in STZ-induced diabetic rats’ hippocampus were detected via responsive commercial kits. Western blot assay were used to determine the protein levels of phospho-phosphatidylinositol 3-kinase (p-PI3K), phospho-Akt (p-Akt), and phospho-glycogen synthase kinase-3β (p-GSK3β). Our results showed that BAC remarkably increased body weight and ChAT activity, decreased blood glucose level and AChE activity as well as improved cognitive deficits in diabetic rats. Additionally, it was also found that treatment with BAC to diabetes obviously stimulated the p-PI3K and p-Akt and inhibited the level of p-GSK3β. Furthermore, the neuronal apoptosis was also prevented after BAC treatment by decreasing caspase-9 and caspase-3 activities in diabetic rats’ hippocampus. It is concluded that BAC exerted beneficial effects against DACD in rats and its neuroprotection might be linked with activating PI3K and Akt phosphorylation accompanied with suppressing the phosphorylated level of GSK3β. These results hint that BAC is likely to be served as an adjuvant therapy to conventional anti-hyperglycemic regimens as well as DACD. PMID:25932128

Variability of blood alcohol content (BAC) determinations: the role of measurement uncertainty, significant figures, and decision rules for compliance assessment in the frame of a multiple BAC threshold law.

PubMed

Zamengo, Luca; Frison, Giampietro; Tedeschi, Gianpaola; Frasson, Samuela; Zancanaro, Flavio; Sciarrone, Rocco

2014-10-01

The measurement of blood-alcohol content (BAC) is a crucial analytical determination required to assess if an offence (e.g. driving under the influence of alcohol) has been committed. For various reasons, results of forensic alcohol analysis are often challenged by the defence. As a consequence, measurement uncertainty becomes a critical topic when assessing compliance with specification limits for forensic purposes. The aims of this study were: (1) to investigate major sources of variability for BAC determinations; (2) to estimate measurement uncertainty for routine BAC determinations; (3) to discuss the role of measurement uncertainty in compliance assessment; (4) to set decision rules for a multiple BAC threshold law, as provided in the Italian Highway Code; (5) to address the topic of the zero-alcohol limit from the forensic toxicology point of view; and (6) to discuss the role of significant figures and rounding errors on measurement uncertainty and compliance assessment. Measurement variability was investigated by the analysis of data collected from real cases and internal quality control. The contribution of both pre-analytical and analytical processes to measurement variability was considered. The resulting expanded measurement uncertainty was 8.0%. Decision rules for the multiple BAC threshold Italian law were set by adopting a guard-banding approach. 0.1 g/L was chosen as cut-off level to assess compliance with the zero-alcohol limit. The role of significant figures and rounding errors in compliance assessment was discussed by providing examples which stressed the importance of these topics for forensic purposes. Copyright © 2014 John Wiley & Sons, Ltd.

Laboratory analysis of risky driving at 0.05% and 0.08% blood alcohol concentration

PubMed Central

Van Dyke, Nicholas A.; Fillmore, Mark T.

2017-01-01

Background The public health costs associated with alcohol-related traffic crashes are a continuing problem for society. One harm reduction strategy has been to employ per se limits for blood alcohol concentrations (BACs) at which drivers can legally operate motor vehicles. This limit is currently 0.08% in all 50 US states. Recently, the National Transportation Safety Board proposed lowering the legal limit to 0.05 % (NTSB, 2013). While research has well-validated the ability of alcohol to impair driving performance and heighten crash-risk at these BACs, relatively little is known about the degree to which alcohol might increase drivers’ risk-taking. Methods Risk-taking was examined in 20 healthy adults who were each tested in a driving simulator following placebo and two doses of alcohol calculated to yield peak BACs of 0.08% and 0.05%, the respective current and proposed BAC limits. The drive test emphasized risk-taking by placing participants in a multiple-lane, high-traffic environment. The primary measure was how close drivers maneuvered relative to other vehicles on the road (i.e., time-to-collision, TTC). Results Alcohol increased risk-taking by decreasing drivers’ TTC at the 0.08% target BAC relative to placebo. Moreover, risk-taking at the 0.05% target was less than risk-taking at 0.08% target BAC. Conclusions These findings provide evidence that reducing the legal BAC limit in the USA to 0.05% would decrease risk-taking among drivers. A clearer understanding of the dose-response relationship between various aspects of driving behaviors, such as drivers’ accepted level of risk while driving, is an important step to improving traffic safety. PMID:28412303

Rapid identification of ESKAPE bacterial strains using an autonomous microfluidic device.

PubMed

Ho, Jack Y; Cira, Nate J; Crooks, John A; Baeza, Josue; Weibel, Douglas B

2012-01-01

This article describes Bacteria ID Chips ('BacChips'): an inexpensive, portable, and autonomous microfluidic platform for identifying pathogenic strains of bacteria. BacChips consist of a set of microchambers and channels molded in the elastomeric polymer, poly(dimethylsiloxane) (PDMS). Each microchamber is preloaded with mono-, di-, or trisaccharides and dried. Pressing the layer of PDMS into contact with a glass coverslip forms the device; the footprint of the device in this article is ∼6 cm(2). After assembly, BacChips are degased under large negative pressure and are stored in vacuum-sealed plastic bags. To use the device, the bag is opened, a sample containing bacteria is introduced at the inlet of the device, and the degased PDMS draws the sample into the central channel and chambers. After the liquid at the inlet is consumed, air is drawn into the BacChip via the inlet and provides a physical barrier that separates the liquid samples in adjacent microchambers. A pH indicator is admixed with the samples prior to their loading, enabling the metabolism of the dissolved saccharides in the microchambers to be visualized. Importantly, BacChips operate without external equipment or instruments. By visually detecting the growth of bacteria using ambient light after ∼4 h, we demonstrate that BacChips with ten microchambers containing different saccharides can reproducibly detect the ESKAPE panel of pathogens, including strains of: Enterococcus faecalis, Enteroccocus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter aerogenes, and Enterobacter cloacae. This article describes a BacChip for point-of-care detection of ESKAPE pathogens and a starting point for designing multiplexed assays that identify bacterial strains from clinical samples and simultaneously determine their susceptibility to antibiotics.

Rapid Identification of ESKAPE Bacterial Strains Using an Autonomous Microfluidic Device

PubMed Central

Ho, Jack Y.; Cira, Nate J.; Crooks, John A.; Baeza, Josue; Weibel, Douglas B.

2012-01-01

This article describes Bacteria ID Chips (‘BacChips’): an inexpensive, portable, and autonomous microfluidic platform for identifying pathogenic strains of bacteria. BacChips consist of a set of microchambers and channels molded in the elastomeric polymer, poly(dimethylsiloxane) (PDMS). Each microchamber is preloaded with mono-, di-, or trisaccharides and dried. Pressing the layer of PDMS into contact with a glass coverslip forms the device; the footprint of the device in this article is ∼6 cm2. After assembly, BacChips are degased under large negative pressure and are stored in vacuum-sealed plastic bags. To use the device, the bag is opened, a sample containing bacteria is introduced at the inlet of the device, and the degased PDMS draws the sample into the central channel and chambers. After the liquid at the inlet is consumed, air is drawn into the BacChip via the inlet and provides a physical barrier that separates the liquid samples in adjacent microchambers. A pH indicator is admixed with the samples prior to their loading, enabling the metabolism of the dissolved saccharides in the microchambers to be visualized. Importantly, BacChips operate without external equipment or instruments. By visually detecting the growth of bacteria using ambient light after ∼4 h, we demonstrate that BacChips with ten microchambers containing different saccharides can reproducibly detect the ESKAPE panel of pathogens, including strains of: Enterococcus faecalis, Enteroccocus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter aerogenes, and Enterobacter cloacae. This article describes a BacChip for point-of-care detection of ESKAPE pathogens and a starting point for designing multiplexed assays that identify bacterial strains from clinical samples and simultaneously determine their susceptibility to antibiotics. PMID:22848451

Correlation between driving-related skill and alcohol use in young-adults from six European countries: the TEN-D by Night Project

PubMed Central

2011-01-01

Background Only few studies with small experimental samples investigated the impact of psychoactive substances on driving performance. We conducted a multicenter international cross-sectional study to evaluate the correlation between alcohol use and driving-related skill as measured by brake reaction time (RT). Methods Before and after the entrance into randomly selected recreational sites from six European countries, all subjects aged 16-35 years, owning a driver license, were asked to compile a structured socio-demographic questionnaire and measure RT (SimuNomad3 driving simulator), breath alcohol concentration (BAC; Drager Alcoltest), and drug use (Oratect III saliva test, only at the exit). Mixed regression modeling was used to evaluate the independent association between RT and alcohol concentration or drug use. Results Before the entrance into the recreational site, 4534 subjects completed all assessments and composed the final sample. Their mean age was 23.1 ± 4.2y; 68.3% were males; 54.7% had BAC > 0 g/L (assumed alcoholics); 7.5% declared illegal drug assumption (mostly cannabis). After the exit, 3019 also completed the second assessment: 71.7% showed BAC > 0 g/L. Controlling for age, gender, educational level, occupation, driver license years, and drug use, BAC was positively associated with RT, achieving significance, however, only when BAC was higher than 0.49 g/L. Significant interaction terms were found between BAC and female gender or drug use, with highest RTs (> 1 sec.) recorded among drug users with BAC > = 1 g/L. Conclusions This field study confirms previous experimental data on the negative impact of alcohol use on driving-related skill, supporting regulations and educational campaigns aimed at discouraging driving after consumption of psychoactive substances. PMID:21722358

A herpes simplex virus 2 glycoprotein D mutant generated by bacterial artificial chromosome mutagenesis is severely impaired for infecting neuronal cells and infects only Vero cells expressing exogenous HVEM.

PubMed

Wang, Kening; Kappel, Justin D; Canders, Caleb; Davila, Wilmer F; Sayre, Dean; Chavez, Mayra; Pesnicak, Lesley; Cohen, Jeffrey I

2012-12-01

We constructed a herpes simplex virus 2 (HSV-2) bacterial artificial chromosome (BAC) clone, bHSV2-BAC38, which contains full-length HSV-2 inserted into a BAC vector. Unlike previously reported HSV-2 BAC clones, the virus genome inserted into this BAC clone has no known gene disruptions. Virus derived from the BAC clone had a wild-type phenotype for growth in vitro and for acute infection, latency, and reactivation in mice. HVEM, expressed on epithelial cells and lymphocytes, and nectin-1, expressed on neurons and epithelial cells, are the two principal receptors used by HSV to enter cells. We used the HSV-2 BAC clone to construct an HSV-2 glycoprotein D mutant (HSV2-gD27) with point mutations in amino acids 215, 222, and 223, which are critical for the interaction of gD with nectin-1. HSV2-gD27 infected cells expressing HVEM, including a human epithelial cell line. However, the virus lost the ability to infect cells expressing only nectin-1, including neuronal cell lines, and did not infect ganglia in mice. Surprisingly, we found that HSV2-gD27 could not infect Vero cells unless we transduced the cells with a retrovirus expressing HVEM. High-level expression of HVEM in Vero cells also resulted in increased syncytia and enhanced cell-to-cell spread in cells infected with wild-type HSV-2. The inability of the HSV2-gD27 mutant to infect neuronal cells in vitro or sensory ganglia in mice after intramuscular inoculation suggests that this HSV-2 mutant might be an attractive candidate for a live attenuated HSV-2 vaccine.

A Herpes Simplex Virus 2 Glycoprotein D Mutant Generated by Bacterial Artificial Chromosome Mutagenesis Is Severely Impaired for Infecting Neuronal Cells and Infects Only Vero Cells Expressing Exogenous HVEM

PubMed Central

Kappel, Justin D.; Canders, Caleb; Davila, Wilmer F.; Sayre, Dean; Chavez, Mayra; Pesnicak, Lesley; Cohen, Jeffrey I.

2012-01-01

We constructed a herpes simplex virus 2 (HSV-2) bacterial artificial chromosome (BAC) clone, bHSV2-BAC38, which contains full-length HSV-2 inserted into a BAC vector. Unlike previously reported HSV-2 BAC clones, the virus genome inserted into this BAC clone has no known gene disruptions. Virus derived from the BAC clone had a wild-type phenotype for growth in vitro and for acute infection, latency, and reactivation in mice. HVEM, expressed on epithelial cells and lymphocytes, and nectin-1, expressed on neurons and epithelial cells, are the two principal receptors used by HSV to enter cells. We used the HSV-2 BAC clone to construct an HSV-2 glycoprotein D mutant (HSV2-gD27) with point mutations in amino acids 215, 222, and 223, which are critical for the interaction of gD with nectin-1. HSV2-gD27 infected cells expressing HVEM, including a human epithelial cell line. However, the virus lost the ability to infect cells expressing only nectin-1, including neuronal cell lines, and did not infect ganglia in mice. Surprisingly, we found that HSV2-gD27 could not infect Vero cells unless we transduced the cells with a retrovirus expressing HVEM. High-level expression of HVEM in Vero cells also resulted in increased syncytia and enhanced cell-to-cell spread in cells infected with wild-type HSV-2. The inability of the HSV2-gD27 mutant to infect neuronal cells in vitro or sensory ganglia in mice after intramuscular inoculation suggests that this HSV-2 mutant might be an attractive candidate for a live attenuated HSV-2 vaccine. PMID:22993162

Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays

PubMed Central

2013-01-01

Background Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. Single nucleotide polymorphisms (SNPs) can be screened in multiplexed format, therefore this marker type lends itself particularly well for medium- to high-throughput applications. Combining the power of multiplex-PCR assays with a multidimensional pooling system may prove to be especially challenging in a polyploid genome. In polyploid genomes two classes of SNPs need to be distinguished, polymorphisms between accessions (intragenomic SNPs) and those differentiating between homoeologous genomes (intergenomic SNPs). We have assessed whether the highly parallel Illumina GoldenGate® Genotyping Assay is suitable for the screening of a BAC library of the polyploid Brassica napus genome. Results A multidimensional screening platform was developed for a Brassica napus BAC library which is composed of almost 83,000 clones. Intragenomic and intergenomic SNPs were included in Illumina’s GoldenGate® Genotyping Assay and both SNP classes were used successfully for screening of the multidimensional BAC pools of the Brassica napus library. An optimized scoring method is proposed which is especially valuable for SNP calling of intergenomic SNPs. Validation of the genotyping results by independent methods revealed a success of approximately 80% for the multiplex PCR-based screening regardless of whether intra- or intergenomic SNPs were evaluated. Conclusions Illumina’s GoldenGate® Genotyping Assay can be efficiently used for screening of multidimensional Brassica napus BAC pools. SNP calling was specifically tailored for the evaluation of BAC pool screening data. The developed scoring method can be implemented independently of plant reference samples. It is demonstrated that intergenomic SNPs represent a powerful tool for BAC library screening of a polyploid genome. PMID:24010766

N-TERMINALLY ELONGATED SpliInx2 AND SpliInx3 REDUCE BACULOVIRUS-TRIGGERED APOPTOSIS VIA HEMICHANNEL CLOSURE.

PubMed

Chen, Ya-Bin; Xiao, Wei; Li, Ming; Zhang, Yan; Yang, Yang; Hu, Jian-Sheng; Luo, Kai-Jun

2016-05-01

The hemichannel and gap junction channel are major portals for the release of factors responsible for the effects of apoptotic cells on the spread of apoptosis to neighboring cells and apoptotic corpse clearance, typically by phagocytes. The N-terminal cytoplasmic domain in the connexins, gap junction proteins in vertebrate, has been implicated in regulating channel closure. However, little is known about how the hemichannel close responds to apoptotic signaling transduction leading to the reduction of neighboring cellular apoptosis in an invertebrate. An insect Bac-to-Bac expression system, pFastBac(TM) HT A, allows us to construct an N-terminally elongated SpliInx2 (Nte-Inx2) and SpliInx3 (Nte-Inx3). Here, we demonstrated that recombinant baculovirus Bac-Nte-Inx2 (reBac-Net-Inx2) and Bac-Nte-Inx3 (reBac-Nte-Inx3) closed the endogenous hemichannel on the Sf9 cell surface. Importantly, primary baculovirus infections significantly caused early apoptosis, and this apoptosis was reduced by hemichannel-closed Sf9 cells at 24-h post-infection (PI). Although N-terminal-elongated residue led to the increase in the phosphorylated sites in both Nte-Inx2 and Nte-Inx3 and an additional transmembrane domain in Nte-Inx3, both the proteins localized on the cell surface, suggesting Nte-Inxs proteins could mediate hemichannel closure. Further supporting evidence showed that hemichannel closure was dependent on N-Inxs expressed by baculovirus polyhedrin promoter, which began to express at 18-24 h PI. These results identify an unconventional function of N-terminal-elongated innexins that could act as a plug to manipulate hemichannel closure and provide a mechanism connecting the effect of hemichannel closure directly to apoptotic signaling transduction from intracellular to extracellular compartment. © 2016 Wiley Periodicals, Inc.

Relevance of Bacteroidales and F-Specific RNA Bacteriophages for Efficient Fecal Contamination Tracking at the Level of a Catchment in France

PubMed Central

Mauffret, Aourell; Caprais, Marie-Paule

2012-01-01

The relevance of three host-associated Bacteroidales markers (HF183, Rum2Bac, and Pig2Bac) and four F-specific RNA bacteriophage genogroups (FRNAPH I to IV) as microbial source tracking markers was assessed at the level of a catchment (Daoulas, France). They were monitored together with fecal indicators (Escherichia coli and enterococci) and chemophysical parameters (rainfall, temperature, salinity, pH, and turbidity) by monthly sampling over 2 years (n = 240 water samples) and one specific sampling following an accidental pig manure spillage (n = 5 samples). During the 2-year regular monitoring, levels of E. coli, enterococci, total F-specific RNA bacteriophages, and the general Bacteroidales marker AllBac were strongly correlated with one another and with Rum2Bac (r = 0.37 to 0.50, P < 0.0001). Their correlations with HF183 and FRNAPH I and II were lower (r = 0.21 to 0.29, P < 0.001 to P < 0.0001), and HF183 and enterococci were associated rather than correlated (Fisher's exact test, P < 0.01). Rum2Bac and HF183 enabled 73% of water samples that had ≥2.7 log10 most probably number (MPN) of E. coli/100 ml to be classified. FRNAPH I and II enabled 33% of samples at this contamination level to be classified. FRNAPH I and II complemented the water sample classification obtained with the two Bacteroidales markers by an additional 8%. Pig2Bac and FRNAPH III and IV were observed in a small number of samples (n = 0 to 4 of 245). The present study validates Rum2Bac and HF183 as relevant tools to trace fecal contamination originating from ruminant or human waste, respectively, at the level of a whole catchment. PMID:22610433

Evaluation of growth based rapid microbiological methods for sterility testing of vaccines and other biological products.

PubMed

Parveen, Seema; Kaur, Simleen; David, Selwyn A Wilson; Kenney, James L; McCormick, William M; Gupta, Rajesh K

2011-10-19

Most biological products, including vaccines, administered by the parenteral route are required to be tested for sterility at the final container and also at various stages during manufacture. The sterility testing method described in the Code of Federal Regulations (21 CFR 610.12) and the United States Pharmacopoeia (USP, Chapter <71>) is based on the observation of turbidity in liquid culture media due to growth of potential contaminants. We evaluated rapid microbiological methods (RMM) based on detection of growth 1) by adenosine triphosphate (ATP) bioluminescence technology (Rapid Milliflex(®) Detection System [RMDS]), and 2) by CO(2) monitoring technologies (BacT/Alert and the BACTEC systems), as alternate sterility methods. Microorganisms representing Gram negative, Gram positive, aerobic, anaerobic, spore forming, slow growing bacteria, yeast, and fungi were prepared in aliquots of Fluid A or a biological matrix (including inactivated influenza vaccines) to contain approximately 0.1, 1, 10 and 100 colony forming units (CFU) in an inoculum of 10 ml. These preparations were inoculated to the specific media required for the various methods: 1) fluid thioglycollate medium (FTM) and tryptic soy broth (TSB) of the compendial sterility method (both membrane filtration and direct inoculation); 2) tryptic soy agar (TSA), Sabouraud dextrose agar (SDA) and Schaedler blood agar (SBA) of the RMDS; 3) iAST and iNST media of the BacT/Alert system and 4) Standard 10 Aerobic/F and Standard Anaerobic/F media of the BACTEC system. RMDS was significantly more sensitive in detecting various microorganisms at 0.1CFU than the compendial methods (p<0.05), whereas the compendial membrane filtration method was significantly more sensitive than the BACTEC and BacT/Alert methods (p<0.05). RMDS detected all microorganisms significantly faster than the compendial method (p<0.05). BacT/Alert and BACTEC methods detected most microorganisms significantly faster than the compendial method (p<0.05), but took almost the same time to detect the slow growing microorganism P. acnes, compared to the compendial method. RMDS using SBA detected all test microorganisms in the presence of a matrix containing preservative 0.01% thimerosal, whereas the BacT/Alert and BACTEC systems did not consistently detect all the test microorganisms in the presence of 0.01% thimerosal. RMDS was compatible with inactivated influenza vaccines and aluminum phosphate or aluminum hydroxide adjuvants at up to 8 mg/ml without any interference in bioluminescence. RMDS was shown to be acceptable as an alternate sterility method taking 5 days as compared to the 14 days required of the compendial method. Isolation of microorganisms from the RMDS was accomplished by re-incubation of membranes with fresh SBA medium and microbial identification was confirmed using the MicroSEQ Identification System. BacT/Alert and BACTEC systems may be applicable as alternate methods to the compendial direct inoculation sterility method for products that do not contain preservatives or anti-microbial agents. Published by Elsevier Ltd.

Questionable Specificity of Genetic Total Faecal Pollution Markers for Integrated Water Quality Monitoring and Source Tracking

NASA Astrophysics Data System (ADS)

Vierheilig, Julia; Reischer, Georg H.; Farnleitner, Andreas H.

2010-05-01

Characterisation of microbial faecal hazards in water is a fundamental aspect for target-orientated water resources management to achieve appropriate water quality for various purposes like water supply or agriculture and thus to minimize related health risks. Nowadays the management of water resources increasingly demands detailed knowledge on the extent and the origin of microbial pollution. Cultivation of standard faecal indicator bacteria, which has been used for over a century to test the microbiological water quality, cannot sufficiently meet these challenges. The abundant intestinal bacterial populations are very promising alternative targets for modern faecal indication systems. Numerous assays for the detection of genetic markers targeting source-specific populations of the phylum Bacteroidetes have been developed in recent years. In some cases markers for total faecal pollution were also proposed in order to relate source-specific marker concentrations to general faecal pollution levels. However, microbial populations in intestinal and non-intestinal systems exhibit a dazzling array of diversity and molecular analysis of microbial faecal pollution has been based on a fragmentary puzzle of very limited sequence information. The aim of this study was to test the available qPCR-based methods detecting genetic Bacteroidetes markers for total faecal pollution in terms of their value and specificity as indicators of faecal pollution. We applied the AllBac (Layton et al., 2006) the BacUni (Kildare et al., 2007) and the Bacteroidetes (Dick and Field, 2004) assays on soil DNA samples. Samples were collected in well characterised karst spring catchments in Austria's Eastern Calcareous Alps. They were at various levels of altitude between 800 and 1800 meters above sea level and from several different habitats (woodland, alpine pastures, krummholz). In addition we tried to choose sampling sites representing a presumptive gradient of faecal pollution levels. For example sites with obvious faecal influence (e.g. right next to a cowpat) were included as well as more pristine sites without faecal influence from large animals (e.g. fenced areas). Surprisingly, results from investigations with the AllBac assay showed concentrations of the total faecal marker in soil in the range of 106 to 109 Marker Equivalents per g of soil, which is equal or only slightly lower than the concentrations of this particular marker in faeces or raw sewage. Preliminary results from the other tested assays seem to confirm that the targeted markers are also highly abundant in soils. In addition, the markers were present in comparable concentrations in soils from pristine locations as well as in soils under the potential influence of faeces giving a strong indication that these methods also target non-intestinal, autochthonous soil populations. In contrast, source-specific markers (ruminant-specific BacR and human-specific BacH, Reischer et al., 2007, 2006) could only be detected in 30 to 50% of the soil samples at concentrations close to the detection limit, which is at least four orders of magnitude lower than in faecal samples of the respective target sources, ruminant animals and humans. The achieved results call the applicability of the proposed qPCR-based assays for total faecal pollution into question. In fact the assays do not seem to be specific for intestinal Bacteroidetes populations at all and the respective marker concentration levels in pristine soils negate their applicability in the investigated areas. This study also emphasizes the need to test the specificity and sensitivity of qPCR-based assays for total faecal pollution on the local level and especially against non-intestinal environmental samples, which might contribute to marker levels in the aquatic compartment. In conclusion there is a strong demand for marker-based detection techniques for total faecal pollution in water quality monitoring and risk assessment but currently none of the tested assays seems to meet the methodical requirements.

Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.

PubMed

Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L

2014-01-23

Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail "neck", are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the "outer ion" site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of CaV high-affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily. © 2013. Published by Elsevier Ltd. All rights reserved.

Impact of providing drinkers with "know your limit" information on drinking and driving: a field experiment.

PubMed

Johnson, Mark B; Clapp, John D

2011-01-01

Given that most effective alcohol harm-reduction laws specify the blood alcohol concentration (BAC) that constitutes illegal behavior (e.g., the .08% breath alcohol concentration legal limit), interventions that allow drinkers to accurately estimate their BACs, and thus better assess their risk, have potential importance to long-term driving-under-the-influence prevention efforts. This study describes a field experiment designed to test the impact on drinking of providing "Know Your Limit" (KYL) BAC estimation cards to individuals in a natural drinking environment. We randomly sampled 1,215 U.S. residents as they entered Mexico for a night of drinking, interviewed them, and randomly assigned them to one of six experimental conditions. Participants were reinterviewed and breath-tested when they returned to the United States. The experimental conditions included providing generic warnings about drinking and driving, giving out gender-specific BAC calculator cards (KYL cards), and providing incentives to moderate their drinking. Cueing participants about the risks of drunk driving resulted in significantly lower BACs (relative to control) for participants who indicated that they would drive home. Providing KYL matrixes did not reduce BACs, and, in fact, some evidence suggests that KYL cards undermined the effect of the warning. KYL information does not appear to be an effective tool for reducing drinking and driving. Implications for prevention and future research are discussed.

Benzalkonium chloride accelerates the formation of the amyloid fibrils of corneal dystrophy-associated peptides.

PubMed

Kato, Yusuke; Yagi, Hisashi; Kaji, Yuichi; Oshika, Tetsuro; Goto, Yuji

2013-08-30

Corneal dystrophies are genetic disorders resulting in progressive corneal clouding due to the deposition of amyloid fibrils derived from keratoepithelin, also called transforming growth factor β-induced protein (TGFBI). The formation of amyloid fibrils is often accelerated by surfactants such as sodium dodecyl sulfate (SDS). Most eye drops contain benzalkonium chloride (BAC), a cationic surfactant, as a preservative substance. In the present study, we aimed to reveal the role of BAC in the amyloid fibrillation of keratoepithelin-derived peptides in vitro. We used three types of 22-residue synthetic peptides covering Leu110-Glu131 of the keratoepithelin sequence: an R-type peptide with wild-type R124, a C-type peptide with C124 associated with lattice corneal dystrophy type I, and a H-type peptide with H124 associated with granular corneal dystrophy type II. The time courses of spontaneous amyloid fibrillation and seed-dependent fibril elongation were monitored in the presence of various concentrations of BAC or SDS using thioflavin T fluorescence. BAC and SDS accelerated the fibrillation of all synthetic peptides in the absence and presence of seeds. Optimal acceleration occurred near the CMC, which suggests that the unstable and dynamic interactions of keratoepithelin peptides with amphipathic surfactants led to the formation of fibrils. These results suggest that eye drops containing BAC may deteriorate corneal dystrophies and that those without BAC are preferred especially for patients with corneal dystrophies.

Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones.

PubMed

Clément, D; Lanaud, C; Sabau, X; Fouet, O; Le Cunff, L; Ruiz, E; Risterucci, A M; Glaszmann, J C; Piffanelli, P

2004-05-01

We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

The role of beaded activated carbon's pore size distribution on heel formation during cyclic adsorption/desorption of organic vapors.

PubMed

Jahandar Lashaki, Masoud; Atkinson, John D; Hashisho, Zaher; Phillips, John H; Anderson, James E; Nichols, Mark

2016-09-05

The effect of activated carbon's pore size distribution (PSD) on heel formation during adsorption of organic vapors was investigated. Five commercially available beaded activated carbons (BAC) with varying PSDs (30-88% microporous) were investigated. Virgin samples had similar elemental compositions but different PSDs, which allowed for isolating the contribution of carbon's microporosity to heel formation. Heel formation was linearly correlated (R(2)=0.91) with BAC micropore volume; heel for the BAC with the lowest micropore volume was 20% lower than the BAC with the highest micropore volume. Meanwhile, first cycle adsorption capacities and breakthrough times correlated linearly (R(2)=0.87 and 0.93, respectively) with BAC total pore volume. Micropore volume reduction for all BACs confirmed that heel accumulation takes place in the highest energy pores. Overall, these results show that a greater portion of adsorbed species are converted into heel on highly microporous adsorbents due to higher share of high energy adsorption sites in their structure. This differs from mesoporous adsorbents (low microporosity) in which large pores contribute to adsorption but not to heel formation, resulting in longer adsorbent lifetime. Thus, activated carbon with high adsorption capacity and high mesopore fraction is particularly desirable for organic vapor application involving extended adsorption/regeneration cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional and genetic analysis of haplotypic sequence variation at the nicastrin genomic locus

PubMed Central

Hamilton, Gillian; Killick, Richard; Lambert, Jean-Charles; Amouyel, Philippe; Carrasquillo, Minerva M.; Pankratz, V. Shane; Graff-Radford, Neill R.; Dickson, Dennis W.; Petersen, Ronald C.; Younkin, Steven G.; Powell, John F.; Wade-Martins, Richard

2013-01-01

Nicastrin (NCSTN) is a component of the γ-secretase complex and therefore potentially a candidate risk gene for Alzheimer's disease. Here, we have developed a novel functional genomics methodology to express common locus haplotypes to assess functional differences. DNA recombination was used to engineer 5 bacterial artificial chromosomes (BACs) to each express a different haplotype of the NCSTN locus. Each NCSTN-BAC was delivered to knockout nicastrin (Ncstn−/−) cells and clonal NCSTN-BAC+/Ncstn−/− cell lines were created for functional analyses. We showed that all NCSTN-BAC haplotypes expressed nicastrin protein and rescued γ-secretase activity and amyloid beta (Aβ) production in NCSTN-BAC+/Ncstn−/− lines. We then showed that genetic variation at the NCSTN locus affected alternative splicing in human postmortem brain tissue. However, there was no robust functional difference between clonal cell lines rescued by each of the 5 different haplotypes. Finally, there was no statistically significant association of NCSTN with disease risk in the 4 cohorts. We therefore conclude that it is unlikely that common variation at the NCSTN locus is a risk factor for Alzheimer's disease. PMID:22405046

A whole-genome, radiation hybrid map of wheat

USDA-ARS?s Scientific Manuscript database

Generating a reference sequence of bread wheat (Triticum aestivum L.) is a challenging task because of its large, highly repetitive and allopolyploid genome. Ordering of BAC- and NGS-based contigs in ongoing wheat genome-sequencing projects primarily uses recombination and comparative genomics-base...

[Interest of a new instrument to assess cognition in schizophrenia: The Brief Assessment of Cognition in Schizophrenia (BACS)].

PubMed

Bralet, M C; Navarre, M; Eskenazi, A M; Lucas-Ross, M; Falissard, B

2008-12-01

An increasing interest in the study of cognition in Schizophrenia has developed within the last few years although cognitive problems have been described in this disorder since the beginning of the 20th century. Presently, various data tend to assert that cognitive disorders are the core disturbance in schizophrenia and that their severity is predictive of the course of the disease. Indeed, studies have shown that the disturbances measured in cognitive tests are neither the consequences of positive or negative symptoms, nor related to motivation or global intellectual deficit, nor to anti-psychotic medication. It is also presently known that the severity of cognitive symptoms is a better indicator of social and functional outcome than the severity of the negative or positive symptoms. The patients who have the most severe cognitive deficits during the first episode of the disease are most likely to present a chronic and severe form later on. The aspects of cognition that are specifically impaired in schizophrenia are verbal memory, working memory, motor function, attention, executive functions, and verbal fluency. Cognitive disturbances are thus very important in several fields of research in schizophrenia such as: understanding the psychopathology, epidemiology (indicators of vulnerability), genetics (endophenotypes), neuro-imaging (including functional neuro-imaging), and psychopharmacology (they can be used as a parameter of evaluation in therapeutic trials with new molecules, or cognitive psychotherapy). LIMITS OF COGNITION ASSESSMENTS: However, there are some methodological limits to these cognitive evaluations. First, schizophrenia is a heterogeneous disease and there are no specificities of the different subgroups in terms of cognition. Secondly, the time chosen to evaluate the abilities of the patient is also a limiting factor. But most of all, the batteries of tests used in different studies are not standardized. BRIEF ASSESSMENT OF COGNITION IN SCHIZOPHRENIA: It is therefore of great interest to create an available and easily used battery of validated tests. This would enable one to measure the different cognitive deficits and to repeat the tests, and assess evolution through longitudinal follow up of the patients. The BACS is a new instrument developed by Keefe et al. in the Department of Psychiatry and Behavioural Sciences at the University of Duke Medical Centre. It evaluates the cognitive dimensions specifically altered in schizophrenia and correlated with the evolution of the disease. This test is simple to use, requiring only paper, pencils and a stopwatch. It can be administered by different carers. The duration of the test session is approximately 35min. This battery of tests was validated on a sample of 150 patients compared with a sample of 50 controls, matched for age, parent education and ethnic groups. This aim of this study is to create a French adaptation of the BACS (translation and back translation approved by the Department of Psychiatry and Behavioural Sciences at the University of Duke Medical Centre) and then to test its easiness of administration and its sensitivity, performing correlation analysis between the French Version of the BACS (version A) and a standard battery. Its adaptation and validation in French would at first be useful for the French-speaking areas and then would add some new data for the pertinence of using the BACS. 35 French stabilized schizophrenic patients were recruited from the inpatient and outpatient facilities at the Clermont-de-L'Oise Mental Health Hospital (Picardie area, France) in Dr Boitard's Psychiatric Department (FJ 5.) Patients were required to meet DSM-IV criteria for schizophrenia or schizoaffective illness. The patients were tested on two separate days by two independent clinicians with less than two weeks between the two assessments. During the first test session, subjects received the French A version of the BACS and during the second session, they were administered the standard battery of cognitive tests including: the Rey Auditory-Verbal learning test, the Wechsler Adult Intelligence Scale, third edition, subtests (Digit inverse sequencing, Digit Symbol-Coding), the Trail-Making A, Verbal Fluency (Controlled Oral Word Association Test, Category Instances), and the Wisconsin Card Sort Test (128 card version). The factor structure of the French BACS A Version was determined by performing a principal components analysis with oblique rotation. The relationship between the French BACS sub-scores and the standard battery sub-scores was determined by calculating Pearson's correlations among the sub-scores, with a level of significance of alpha<0.05. All the 35 patients completed the standard battery and each subtest of the French BACS A Version without interruption and with good understanding of the instructions. The average duration of the BACS test sessions was 36.51min (S.D.=12.14.) compared to the standard battery in which the sessions lasted more than one hour with more difficulty during the Wisconsin tests. The factor analysis conducted on the data collected from patients suggests that there is a single dimension, a factor of general cognitive performance, which accounted for the greatest amount of variance. The BACS thus permits an assessment of overall cognitive function as a global score, more than some individual specific cognitive domains. The sub-scores from the French BACS A Version were strongly correlated with the standard battery corresponding sub-scores. We observed significant correlations for all the subtests evaluating: verbal memory (Pearson=0.83; p<0.001; IC [0.69; 0.91]), working memory (Pearson=0.67; p<0.001; IC[0.43; 0.80]), verbal fluency (semantic: Pearson=0.64; p<0.001; IC[0.40; 0.80]), alphabetical (Pearson=0.87; p<0.001;IC[0.77; 0.93]), attention and speed of information processing (Pearson=0.69; p<0.001; IC[0.47; 0.83]), executive function (Pearson=0.64; p<0.001; IC[0.39; 0.80]). We almost found a significant correlation for motor speed (Pearson=-0. 32; p=0.06; IC [-0.59; -0.014]). The French adaptation of the BACS scale is easier to use in schizophrenic patients with French as mother tongue, with a completion rate equal to 1, and also with less than 35min to complete and check. We obtained significant correlations for all domains except motor speed, which is almost significant. The BACS is as sensitive to cognitive impairment in patients with schizophrenia as a standard battery of tests that required over 2h to complete. Moreover, these results demonstrate that the BACS, the global score of which may be the most powerful indicator of functional outcome, can also be a good neuropsychological instrument for assessing global cognition in patients with schizophrenia.

Blood alcohol concentration in fatally injured drivers and the efficacy of alcohol policies of the new law on road traffic safety: A retrospective 10-year study in autonomous province of Vojvodina, Republic of Serbia.

PubMed

Petković, Stojan; Palić, Kristina; Samojlik, Isidora

2016-08-17

The aim of this study was primarily to evaluate inebriated fatally injured drivers (FIDs) according to blood alcohol concentration (BAC) in a 10-year period (2004-2013) in Autonomous Province (AP) of Vojvodina, Republic of Serbia, to analyze the efficacy of alcohol polices in the new law on road traffic safety through changes in the number of inebriated FIDs before and after implementation of the law, as well as to identify factors that influence the occurrence of FIDs with BACs above the legal limit. All data for this retrospective study were obtained from the Centre of Forensic Medicine, Toxicology and Molecular Genetics of Clinical Centre of Vojvodina, Novi Sad. Autopsy records for each case included age, gender, BAC, type of vehicle, and date of accident (year, month, and recalculated day of the week). BAC was determined by gas chromatography with flame ionization detection. Statistical analysis was carried out by chi-square tests and Student's t test, with P < .05 as a statistical significance, and multiple binary logistic regression. Of the 354 inebriated FIDs (60% of all FIDs), the majority had BACs between of 0.031 and 0.3 mg/ml (28%), followed by those with BAC > 2.01 mg/ml (23%). The average BAC of those driving under the influence of alcohol (DUIA) for the whole period was 1.235 ± 1.00 mg/ml and the average number of DUIA/year was 35. Among the total number of FIDs there were significantly more males (93.7%; P < .001) than females (6.3%), though the distribution of intoxicated men and women was not different (P > .05). There was a statistically significant difference in the distribution of sober and inebriated FIDs according to age (P < .001) with the predominance of inebriated FIDs between 21 and 30 years. Although gender and age were found to be significant predictors of BAC above legal limit in FIDs, the area under the receiver operating characteristics (ROC) curve showed that the model had poor discrimination (ROC = 0.673). Of all observed FIDs, 65 cases per year were attributed to the first 5-year period (2004-2009) and 49 to the second 5-year (2010-2013) period, which indicates that there was no statistically significant decrease in the number of FIDs after implementation of the new law. The highest number of intoxicated FIDs during the period in AP Vojvodina were mildly and completely inebriated. In the 4-year post-policy period (2010-2013), the number of FIDs and average BAC levels of inebriated FIDs did not significantly change. The abolition of a permissible BAC should be considered.

Global Genomic Diversity of Oryza sativa Varieties Revealed by Comparative Physical Mapping

PubMed Central

Wang, Xiaoming; Kudrna, David A.; Pan, Yonglong; Wang, Hao; Liu, Lin; Lin, Haiyan; Zhang, Jianwei; Song, Xiang; Goicoechea, Jose Luis; Wing, Rod A.; Zhang, Qifa; Luo, Meizhong

2014-01-01

Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html). PMID:24424778

Preparation of BAC libraries from marine microbial populations.

PubMed

Sabehi, Gazalah; Béjà, Oded

2013-01-01

A protocol is presented here for the construction of BAC (bacterial artificial chromosome) libraries from planktonic microbial communities collected in marine environments. The protocol describes the collection and preparation of the planktonic microbial cells, high molecular weight DNA purification from those cells, the preparation of the BAC vector, and the special ligation and electrotransformation procedures required for successful library preparation. With small modifications, this protocol can be applied to microbes collected from other environments. © 2013 Elsevier Inc. All rights reserved.

23 CFR 1225.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 210 liters of breath. (b) ALR means either administrative license revocation or administrative license suspension. (c) BAC means either blood or breath alcohol concentration. (d) BAC per se law means a law that...

Estimation of Pig Fecal Contamination in a River Catchment by Real-Time PCR Using Two Pig-Specific Bacteroidales 16S rRNA Genetic Markers▿

PubMed Central

Mieszkin, Sophie; Furet, Jean-Pierre; Corthier, Gérard; Gourmelon, Michèle

2009-01-01

The microbiological quality of coastal or river water can be affected by fecal contamination from human or animal sources. To discriminate pig fecal pollution from other pollution, a library-independent microbial source tracking method targeting Bacteroidales host-specific 16S rRNA gene markers by real-time PCR was designed. Two pig-specific Bacteroidales markers (Pig-1-Bac and Pig-2-Bac) were designed using 16S rRNA gene Bacteroidales clone libraries from pig feces and slurry. For these two pig markers, 98 to 100% sensitivity and 100% specificity were obtained when tested by TaqMan real-time PCR. A decrease in the concentrations of Pig-1-Bac and Pig-2-Bac markers was observed throughout the slurry treatment chain. The two newly designed pig-specific Bacteroidales markers, plus the human-specific (HF183) and ruminant-specific (BacR) Bacteroidales markers, were then applied to river water samples (n = 24) representing 14 different sites from the French Daoulas River catchment (Brittany, France). Pig-1-Bac and Pig-2-Bac were quantified in 25% and 62.5%, respectively, of samples collected around pig farms, with concentrations ranging from 3.6 to 4.1 log10 copies per 100 ml of water. They were detected in water samples collected downstream from pig farms but never detected near cattle farms. HF183 was quantified in 90% of water samples collected downstream near Daoulas town, with concentrations ranging between 3.6 and 4.4 log10 copies per 100 ml of water, and BacR in all water samples collected around cattle farms, with concentrations ranging between 4.6 and 6.0 log10 copies per 100 ml of water. The results of this study highlight that pig fecal contamination was not as frequent as human or bovine fecal contamination and that fecal pollution generally came from multiple origins. The two pig-specific Bacteroidales markers can be applied to environmental water samples to detect pig fecal pollution. PMID:19329663

A written self-help intervention for depressed adults comparing behavioural activation combined with physical activity promotion with a self-help intervention based upon behavioural activation alone: study protocol for a parallel group pilot randomised controlled trial (BAcPAc).

PubMed

Farrand, Paul; Pentecost, Claire; Greaves, Colin; Taylor, Rod S; Warren, Fiona; Green, Colin; Hillsdon, Melvyn; Evans, Phil; Welsman, Jo; Taylor, Adrian H

2014-05-29

Challenges remain to find ways to support patients with depression who have low levels of physical activity (PA) to overcome perceived barriers and enhance the perceived value of PA for preventing future relapse. There is an evidence-base for behavioural activation (BA) for depression, which focuses on supporting patients to restore activities that have been avoided, but practitioners have no specific training in promoting PA. We aimed to design and evaluate an integrated BA and PA (BAcPAc) practitioner-led, written, self-help intervention to enhance both physical and mental health. This study is informed by the Medical Research Council Complex Intervention Framework and describes a protocol for a pilot phase II randomised controlled trial (RCT) to test the feasibility and acceptability of the trial methods to inform a definitive phase III RCT. Following development of the augmented written self-help intervention (BAcPAc) incorporating behavioural activation with physical activity promotion, depressed adults are randomised to receive up to 12 sessions over a maximum of 4 months of either BAcPAc or behavioural activation alone within a written self-help format, which represents treatment as usual. The study is located within two 'Improving Access to Psychological Therapies' services in South West England, with both written self-help interventions supported by mental health paraprofessionals. Measures assessed at 4, 9, and 12 month follow-up include the following: CIS-R, PHQ-9, accelerometer recorded (4 months only) and self-reported PA, body mass index, blood pressure, Insomnia Severity Index, quality of life, and health and social care service use. Process evaluation will include analysis of recorded support sessions and patient and practitioner interviews. At the time of writing the study has recruited 60 patients. The feasibility outcomes will inform a definitive RCT to assess the clinical and cost-effectiveness of the augmented BAcPAc written self-help intervention to reduce depression and depressive relapse, and bring about improvements across a range of physical health outcomes. Current Controlled Trials ISRCTN74390532, 26.03.2013.

Comparison of ethanol concentrations in venous blood and end-expired breath during a controlled drinking study.

PubMed

Jones, A W; Andersson, L

2003-03-12

Concentration-time profiles of ethanol were determined for venous whole blood and end-expired breath during a controlled drinking experiment in which healthy men (n=9) and women (n=9) drank 0.40-0.65 g ethanol per kg body weight in 20-30 min. Specimens of blood and breath were obtained for analysis of ethanol starting at 50-60 min post-dosing and then every 30-60 min for 3-6 h. This protocol furnished 130 blood-breath pairs for statistical evaluation. Blood-ethanol concentration (BAC, mg/g) was determined by headspace gas chromatography and breath-ethanol concentration (BrAC, mg/2l) was determined with a quantitative infrared analyzer (Intoxilyzer 5000S), which is the instrument currently used in Sweden for legal purposes. In 18 instances the Intoxilyzer 5000S gave readings of 0.00 mg/2l whereas the actual BAC was 0.08 mg/g on average (range 0.04-0.15 mg/g). The remaining 112 blood- and breath-alcohol measurements were highly correlated (r=0.97) and the regression relationship was BAC=0.10+0.91BrAC and the residual standard deviation (S.D.) was 0.042 mg/g (8.4%). The slope (0.91+/-0.0217) differed significantly from unity being 9% low and the intercept (0.10+/-0.0101) deviated from zero (t=10.2, P<0.001), indicating the presence of both proportional and constant bias, respectively. The mean bias (BAC - BrAC) was 0.068 mg/g and the 95% limits of agreement were -0.021 and 0.156 mg/g. The average BAC/BrAC ratio was 2448+/-540 (+/-S.D.) with a median of 2351 and 2.5th and 97.5th percentiles of 1836 and 4082. We found no significant gender-related differences in BAC/BrAC ratios, being 2553+/-576 for men and 2417+/-494 for women (t=1.34, P>0.05). The mean rate of ethanol disappearance from blood was 0.157+/-0.021 mg/(g per hour), which was very close to the elimination rate from breath of 0.161+/-0.021 mg/(2l per hour) (P>0.05). Breath-test results obtained with Intoxilyzer 5000S (mg/2l) were generally less than the coexisting concentrations of ethanol in venous blood (mg/g), which gives an advantage to the suspect who provides breath compared with blood in cases close to a threshold alcohol limit.

Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray

PubMed Central

von Schalburg, Kristian R; Rise, Matthew L; Cooper, Glenn A; Brown, Gordon D; Gibbs, A Ross; Nelson, Colleen C; Davidson, William S; Koop, Ben F

2005-01-01

Background We have developed and fabricated a salmonid microarray containing cDNAs representing 16,006 genes. The genes spotted on the array have been stringently selected from Atlantic salmon and rainbow trout expressed sequence tag (EST) databases. The EST databases presently contain over 300,000 sequences from over 175 salmonid cDNA libraries derived from a wide variety of tissues and different developmental stages. In order to evaluate the utility of the microarray, a number of hybridization techniques and screening methods have been developed and tested. Results We have analyzed and evaluated the utility of a microarray containing 16,006 (16K) salmonid cDNAs in a variety of potential experimental settings. We quantified the amount of transcriptome binding that occurred in cross-species, organ complexity and intraspecific variation hybridization studies. We also developed a methodology to rapidly identify and confirm the contents of a bacterial artificial chromosome (BAC) library containing Atlantic salmon genomic DNA. Conclusion We validate and demonstrate the usefulness of the 16K microarray over a wide range of teleosts, even for transcriptome targets from species distantly related to salmonids. We show the potential of the use of the microarray in a variety of experimental settings through hybridization studies that examine the binding of targets derived from different organs and tissues. Intraspecific variation in transcriptome expression is evaluated and discussed. Finally, BAC hybridizations are demonstrated as a rapid and accurate means to identify gene content. PMID:16164747

The effect of resveratrol on protecting corneal epithelial cells from cytotoxicity caused by moxifloxacin and benzalkonium chloride.

PubMed

Tsai, Tzu-Yun; Chen, Ta-Ching; Wang, I-Jong; Yeh, Chao-Yuan; Su, Ming-Jai; Chen, Ruey-Hua; Tsai, Tzu-Hsun; Hu, Fung-Rong

2015-02-10

Moxifloxacin (MOX), a fourth generation fluoroquinolone (FQ), has a wide antibacterial spectrum, but may show cytotoxicity characterized by high productions of reactive oxygen species (ROS). This study investigated the protective role of a common antioxidant agent, resveratrol (trans-3,5,4'-trihydroxystilbene), against the cytotoxicity caused by MOX. Experiments were performed with a human corneal epithelial cell line (HCECs; ATCC-CRL-11515). Another commonly used FQ, levofloxacin (LEV), and the most commonly used preservatives, benzalkonium chloride (BAC), were also used for comparison with MOX. Cell viability and morphologic changes after treatment were evaluated with trypan blue exclusion assay, propidium iodine/annexin V-FITC staining, and flow cytometry. Chemiluminescence immunoassay was used for ROS quantification. MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay, wound healing assay, and intracellular detections of oxidative stress were performed to evaluate the effects of resveratrol. The MOX group, similar to the BAC group, showed significant cell shrinkage and death compared with the LEV group. High ROS production in HCECs of MOX group was observed both by chemiluminescence immunoassay and intracellular images. Within the observations of MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay, live cell images, and wound healing process in vitro, the cytotoxic effects of the MOX and BAC groups were opposed by resveratrol. Human corneal epithelial cells pretreated with resveratrol demonstrated better cell viability and healing rate in the early stage. The protective effects of antioxidant agents indicate that MOX, similar to BAC, causes oxidative stress-related cell damage. The results also inspired us to think about a "supplementary regimen" to increase safety and decrease the adverse effect in the treatment of corneal infections. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

Adenocarcinoma with BAC Features Presented as the Nonsolid Nodule Is Prone to Be False-Negative on 18F-FDG PET/CT

PubMed Central

Wu, Hu-bing; Wang, Lijuan; Wang, Quan-shi; Han, Yan-jian; Li, Hong-sheng; Zhou, Wen-lan; Tian, Ying

2015-01-01

Purpose. The present study investigated which type of adenocarcinoma with BAC features was prone to be false-negative on 18F-FDG PET/CT. Materials and Methods. A retrospective study was performed on 51 consecutive patients with localized adenocarcinoma with BAC features. CT and PET were assessed for lesion size, GGO percentage, and SUVmax. Lesions with FDG uptake the same as or more than mediastinal blood-pool activity were considered as PET-positive. Results. Of the 51 cases, 19.6% presented as pure GGO nodules, 31.4% as mixed nodules, and 49.0% as solid nodules. None of the pure GGO nodules was 18F-FDG avid, compared with 37.5% of mixed nodules and 96.0% of solid nodules (χ 2 = 31.55, P = 0.000). In the mixed nodule group, SUVmax was negatively correlated with GGO percentage (r = −0.588; P = 0.021). The positive detection rate of 18F-FDG PET/CT was 50.0%, 55.6%, and 100% in tumors 1.1–2.0 cm, 2.1–3.0 cm, and >3.0 cm in diameter, respectively (χ 2 = 5.815, P = 0.055). General linear model factor analysis showed that the GGO was an important factor contributing to false-negative PET/CT results (F = 23.992, P = 0.000), but lesion size was not (F = 0.602, P = 0.866). Conclusions. The present study indicated that the adenocarcinoma with BAC features presented as nonsolid nodule is prone to be false negative on 18F-FDG PET/CT. PMID:25879020

Reprint of "evolution of specific immunity in shrimp - a vaccination perspective against white spot syndrome virus".

PubMed

Syed Musthaq, Syed Khader; Kwang, Jimmy

2015-02-01

Invertebrates lack true adaptive immunity and it solely depends on the primitive immunity called innate immunity. However, various innate immune molecules and mechanisms are identified in shrimp that plays potential role against invading bacterial, fungal and viral pathogens. Perceiving the shrimp innate immune mechanisms will contribute in developing effective vaccine strategies against major shrimp pathogens. Hence this review intends to explore the innate immune molecules of shrimp with suitable experimental evidences together with the evolution of "specific immune priming" of invertebrates. In addition, we have emphasized on the development of an effective vaccine strategy against major shrimp pathogen, white spot syndrome virus (WSSV). The baculovirus displayed rVP28 (Bac-VP28), a major envelope protein of WSSV was utilized to study its vaccine efficacy by oral route. A significant advantage of this baculovirus expression cassette is the use of WSSV-immediate early 1 (ie1) promoter that derived the abundant expression of rVP28 protein at the early stage of the infection in insect cell. The orally vaccinated shrimp with Bac-VP28 transduced successfully in the shrimp cells as well as provided highest survival rate. In support to our vaccine efficacy we analysed Pattern Recognition Proteins (PRPs) β-1,3 glucan lipopolysaccharides (LGBP) and STAT gene profiles in the experimental shrimp. Indeed, the vaccination of shrimp with Bac-VP28 demonstrated some degree of specificity with enhanced survival rate when compared to control vaccination with Bac-wt. Hence it is presumed that the concept of "specific immune priming" in relevant to shrimp immunity is possible but may not be common to all shrimp pathogens. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolution of specific immunity in shrimp - a vaccination perspective against white spot syndrome virus.

PubMed

Syed Musthaq, Syed Khader; Kwang, Jimmy

2014-10-01

Invertebrates lack true adaptive immunity and it solely depends on the primitive immunity called innate immunity. However, various innate immune molecules and mechanisms are identified in shrimp that plays potential role against invading bacterial, fungal and viral pathogens. Perceiving the shrimp innate immune mechanisms will contribute in developing effective vaccine strategies against major shrimp pathogens. Hence this review intends to explore the innate immune molecules of shrimp with suitable experimental evidences together with the evolution of "specific immune priming" of invertebrates. In addition, we have emphasized on the development of an effective vaccine strategy against major shrimp pathogen, white spot syndrome virus (WSSV). The baculovirus displayed rVP28 (Bac-VP28), a major envelope protein of WSSV was utilized to study its vaccine efficacy by oral route. A significant advantage of this baculovirus expression cassette is the use of WSSV-immediate early 1 (ie1) promoter that derived the abundant expression of rVP28 protein at the early stage of the infection in insect cell. The orally vaccinated shrimp with Bac-VP28 transduced successfully in the shrimp cells as well as provided highest survival rate. In support to our vaccine efficacy we analysed Pattern Recognition Proteins (PRPs) β-1,3 glucan lipopolysaccharides (LGBP) and STAT gene profiles in the experimental shrimp. Indeed, the vaccination of shrimp with Bac-VP28 demonstrated some degree of specificity with enhanced survival rate when compared to control vaccination with Bac-wt. Hence it is presumed that the concept of "specific immune priming" in relevant to shrimp immunity is possible but may not be common to all shrimp pathogens. Copyright © 2014 Elsevier Ltd. All rights reserved.

BacDive--The Bacterial Diversity Metadatabase in 2016.

PubMed

Söhngen, Carola; Podstawka, Adam; Bunk, Boyke; Gleim, Dorothea; Vetcininova, Anna; Reimer, Lorenz Christian; Ebeling, Christian; Pendarovski, Cezar; Overmann, Jörg

2016-01-04

BacDive-the Bacterial Diversity Metadatabase (http://bacdive.dsmz.de) provides strain-linked information about bacterial and archaeal biodiversity. The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. The majority of data is manually annotated and curated. Currently (with release 9/2015), BacDive covers 53 978 strains. Newly implemented RESTful web services provide instant access to the content in machine-readable XML and JSON format. Besides an overall increase of data content, BacDive offers new data fields and features, e.g. the search for gene names, plasmids or 16S rRNA in the advanced search, as well as improved linkage of entries to external life science web resources. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Size matters: versatile use of PiggyBac transposons as a genetic manipulation tool.

PubMed

Kim, Adele; Pyykko, Ilmari

2011-08-01

Transposons have been promising elements for gene integration, and the Sleeping Beauty (SB) system has been the major one for many years, although there have been several other transposon systems available, for example, Tol2. However, recently another system known as PiggyBac (PB) has been introduced and developed for fulfilling the same purposes, for example, mutagenesis, transgenesis and gene therapy and in some cases with improved transposition efficiency and advantages over the Sleeping Beauty transposon system, although improved hyperactive transposase has highly increased the transposition efficacy for SB. The PB systems have been used in many different scientific research fields; therefore, the purpose of this review is to describe some of these versatile uses of the PiggyBac system to give readers an overview on the usage of PiggyBac system.

What proof is in your Christmas pudding? Is caring under the influence possible?

PubMed

Brieger, Daniel G; Amir, Amaleena B; Punch, Gratian J; Lim, Christopher S H; Toh, James

2014-12-11

To determine the ethanol concentration of commonly available Christmas puddings, and to extrapolate the blood alcohol content (BAC) of typical health care professionals after Christmas lunch at the hospital. We conducted fractional distillation of Christmas puddings and analysed the distillate for ethanol content. We then applied standard pharmacological and physiological assumptions to assess predicted BAC in typical male and female health care professionals at our hospital. Ethanol concentration of each pudding; estimated BAC of health care professionals after ingestion and at the end of a 30-minute lunch break. The concentration of ethanol in common Christmas puddings ranged from 0.260 to 1.685 g per 125 mg slice. The concentration of ethanol per pudding was not greater than the stipulated specifications on the packaging, where shown. After pudding ingestion, the theoretical BAC of a typical 70 kg male and 60 kg female health care professional ranged from 0.001 to 0.004 g/dL and from 0.001 to 0.006 g/dL, respectively. Neither male nor female staff had a predicted BAC > 0.000 g/dL by the end of the lunch break. Christmas puddings contain ethanol that does not all evaporate during the cooking process. However, the rise in BAC after ingestion of a typical slice of Christmas pudding was negligible and unlikely to affect work performance or safety or impair a health care worker's ability to make complex decisions.

Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

PubMed Central

Schmeisser, Falko; Weir, Jerry P

2007-01-01

Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC) technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2) BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. While the BAC mutagenesis procedure is a powerful method to generate HSV-2 recombinants, particularly in the absence of selective marker in eukaryotic culture, the mutagenesis procedure is still difficult and cumbersome. Results Here we describe the incorporation of a phage lambda recombination system into an allele replacement vector. This strategy enables any DNA fragment containing the phage attL recombination sites to be efficiently inserted into the attR sites of the allele replacement vector using phage lambda clonase. We also describe how the incorporation of EGFP into the allele replacement vector can facilitate the selection of the desired cross-over recombinant BACs when the allele replacement reaction is a viral gene deletion. Finally, we incorporate the lambda phage recombination sites directly into an HSV-2 BAC vector for direct recombination of gene cassettes using the phage lambda clonase-driven recombination reaction. Conclusion Together, these improvements to the techniques of HSV BAC mutagenesis will facilitate the construction of recombinant herpes simplex viruses and viral vectors. PMID:17501993

Best-practices approach to determination of blood alcohol concentration (BAC) at specific time points: Combination of ante-mortem alcohol pharmacokinetic modeling and post-mortem alcohol generation and transport considerations.

PubMed

Cowan, Dallas M; Maskrey, Joshua R; Fung, Ernest S; Woods, Tyler A; Stabryla, Lisa M; Scott, Paul K; Finley, Brent L

2016-07-01

Alcohol concentrations in biological matrices offer information regarding an individual's intoxication level at a given time. In forensic cases, the alcohol concentration in the blood (BAC) at the time of death is sometimes used interchangeably with the BAC measured post-mortem, without consideration for alcohol concentration changes in the body after death. However, post-mortem factors must be taken into account for accurate forensic determination of BAC prior to death to avoid incorrect conclusions. The main objective of this work was to describe best practices for relating ante-mortem and post-mortem alcohol concentrations, using a combination of modeling, empirical data and other qualitative considerations. The Widmark modeling approach is a best practices method for superimposing multiple alcohol doses ingested at various times with alcohol elimination rate adjustments based on individual body factors. We combined the selected ante-mortem model with a suggestion for an approach used to roughly estimate changes in BAC post-mortem, and then analyzed the available data on post-mortem alcohol production in human bodies and potential markers for alcohol production through decomposition and putrefaction. Hypothetical cases provide best practice approaches as an example for determining alcohol concentration in biological matrices ante-mortem, as well as potential issues encountered with quantitative post-mortem approaches. This study provides information for standardizing BAC determination in forensic toxicology, while minimizing real world case uncertainties. Copyright © 2016 Elsevier Inc. All rights reserved.

MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes.

PubMed

Gradia, Scott D; Ishida, Justin P; Tsai, Miaw-Sheue; Jeans, Chris; Tainer, John A; Fuss, Jill O

2017-01-01

Recombinant expression of large, multiprotein complexes is essential and often rate limiting for determining structural, biophysical, and biochemical properties of DNA repair, replication, transcription, and other key cellular processes. Baculovirus-infected insect cell expression systems are especially well suited for producing large, human proteins recombinantly, and multigene baculovirus systems have facilitated studies of multiprotein complexes. In this chapter, we describe a multigene baculovirus system called MacroBac that uses a Biobricks-type assembly method based on restriction and ligation (Series 11) or ligation-independent cloning (Series 438). MacroBac cloning and assembly is efficient and equally well suited for either single subcloning reactions or high-throughput cloning using 96-well plates and liquid handling robotics. MacroBac vectors are polypromoter with each gene flanked by a strong polyhedrin promoter and an SV40 poly(A) termination signal that minimize gene order expression level effects seen in many polycistronic assemblies. Large assemblies are robustly achievable, and we have successfully assembled as many as 10 genes into a single MacroBac vector. Importantly, we have observed significant increases in expression levels and quality of large, multiprotein complexes using a single, multigene, polypromoter virus rather than coinfection with multiple, single-gene viruses. Given the importance of characterizing functional complexes, we believe that MacroBac provides a critical enabling technology that may change the way that structural, biophysical, and biochemical research is done. © 2017 Elsevier Inc. All rights reserved.

Removal of anaerobic soluble microbial products in a biological activated carbon reactor.

PubMed

Dong, Xiaojing; Zhou, Weili; He, Shengbing

2013-09-01

The soluble microbial products (SMP) in the biological treatment effluent are generally of great amount and are poorly biodegradable. Focusing on the biodegradation of anaerobic SMP, the biological activated carbon (BAC) was introduced into the anaerobic system. The experiments were conducted in two identical lab-scale up-flow anaerobic sludge blanket (UASB) reactors. The high strength organics were degraded in the first UASB reactor (UASB1) and the second UASB (UASB2, i.e., BAC) functioned as a polishing step to remove SMP produced in UASB1. The results showed that 90% of the SMP could be removed before granular activated carbon was saturated. After the saturation, the SMP removal decreased to 60% on the average. Analysis of granular activated carbon adsorption revealed that the main role of SMP removal in BAC reactor was biodegradation. A strain of SMP-degrading bacteria, which was found highly similar to Klebsiella sp., was isolated, enriched and inoculated back to the BAC reactor. When the influent chemical oxygen demand (COD) was 10,000 mg/L and the organic loading rate achieved 10 kg COD/(m3 x day), the effluent from the BAC reactor could meet the discharge standard without further treatment. Anaerobic BAC reactor inoculated with the isolated Klebsiella was proved to be an effective, cheap and easy technical treatment approach for the removal of SMP in the treatment of easily-degradable wastewater with COD lower than 10,000 mg/L.

Technical Note: Could benzalkonium chloride be a suitable alternative to mercuric chloride for preservation of seawater samples?

NASA Astrophysics Data System (ADS)

Gloël, J.; Robinson, C.; Tilstone, G. H.; Tarran, G.; Kaiser, J.

2015-08-01

Instrumental equipment unsuitable or unavailable for fieldwork as well as lack of ship space can necessitate the preservation of seawater samples prior to analysis in a shore-based laboratory. Mercuric chloride (HgCl2) is routinely used for such preservation, but its handling and subsequent disposal incur significant risks and expense. Benzalkonium chloride (BAC) has been used previously for freshwater samples. Here, we assess BAC as a less hazardous alternative microbial inhibitor for marine samples prior to the measurement of oxygen-to-argon (O2/Ar) ratios, as used for the determination of plankton net community production. BAC at a concentration of 50 mg dm-3 inhibited microbial activity for at least three days in seawater with chlorophyll a (Chl a) concentrations up to 1 mg m-3, possibly longer when Chl a concentrations were lower. BAC concentrations of 100 and 200 mg dm-3 were no more effective than 50 mg dm-3. With fewer risks to human health and the environment, and no requirement for expensive waste disposal, BAC could be a viable alternative to HgCl2 for short-term preservation of seawater samples, but is not a replacement for HgCl2 in the case of oxygen triple isotope analysis, which requires storage over weeks to months. In any event, further tests on a case-by-case basis should be undertaken if use of BAC was considered, since its inhibitory activity may depend on concentration and composition of the microbial community.

Benzalkonium Chloride Accelerates the Formation of the Amyloid Fibrils of Corneal Dystrophy-associated Peptides*

PubMed Central

Kato, Yusuke; Yagi, Hisashi; Kaji, Yuichi; Oshika, Tetsuro; Goto, Yuji

2013-01-01

Corneal dystrophies are genetic disorders resulting in progressive corneal clouding due to the deposition of amyloid fibrils derived from keratoepithelin, also called transforming growth factor β-induced protein (TGFBI). The formation of amyloid fibrils is often accelerated by surfactants such as sodium dodecyl sulfate (SDS). Most eye drops contain benzalkonium chloride (BAC), a cationic surfactant, as a preservative substance. In the present study, we aimed to reveal the role of BAC in the amyloid fibrillation of keratoepithelin-derived peptides in vitro. We used three types of 22-residue synthetic peptides covering Leu110-Glu131 of the keratoepithelin sequence: an R-type peptide with wild-type R124, a C-type peptide with C124 associated with lattice corneal dystrophy type I, and a H-type peptide with H124 associated with granular corneal dystrophy type II. The time courses of spontaneous amyloid fibrillation and seed-dependent fibril elongation were monitored in the presence of various concentrations of BAC or SDS using thioflavin T fluorescence. BAC and SDS accelerated the fibrillation of all synthetic peptides in the absence and presence of seeds. Optimal acceleration occurred near the CMC, which suggests that the unstable and dynamic interactions of keratoepithelin peptides with amphipathic surfactants led to the formation of fibrils. These results suggest that eye drops containing BAC may deteriorate corneal dystrophies and that those without BAC are preferred especially for patients with corneal dystrophies. PMID:23861389

Precipitating Circumstances of Suicide and Alcohol Intoxication among U.S. Ethnic Groups

PubMed Central

Caetano, Raul; Kaplan, Mark S.; Huguet, Nathalie; Conner, Kenneth; McFarland, Bentson H.; Giesbrecht, Norman; Nolte, Kurt B.

2015-01-01

Background To assess the prevalence of nine different types of precipitating circumstances among suicide decedents, and examine the association between circumstances and post-mortem blood alcohol content (BAC ≥ 0.08 g/dl.) across U.S. ethnic groups. Methods Data come from the restricted 2003-2011 National Violent Death Reporting System (NVDRS), with post-mortem information on 59,384 male and female suicide decedents for 17 states of the U.S. Results Among men, precipitating circumstances statistically associated with a BAC ≥ 0.08 g/dl were physical health and job problems for Blacks, and experiencing a crisis, physical health problems and intimate partner problem for Hispanics. Among women, the only precipitating circumstance associated with a BAC ≥ 0.08 g/dl was substance abuse problems other than alcohol for Blacks. The number of precipitating circumstances present before the suicide was negatively associated with a BAC ≥ 0.08 g/dl for Whites, Blacks and Hispanics. Conclusions Selected precipitating circumstances were associated with a BAC ≥ 0.08 g/dl, and the strongest determinant of this level of alcohol intoxication prior to suicide among all ethnic groups was the presence of an alcohol problem. PMID:26173709

Comparative Analysis of WRKY Genes Potentially Involved in Salt Stress Responses in Triticum turgidum L. ssp. durum.

PubMed

Yousfi, Fatma-Ezzahra; Makhloufi, Emna; Marande, William; Ghorbel, Abdel W; Bouzayen, Mondher; Bergès, Hélène

2016-01-01

WRKY transcription factors are involved in multiple aspects of plant growth, development and responses to biotic stresses. Although they have been found to play roles in regulating plant responses to environmental stresses, these roles still need to be explored, especially those pertaining to crops. Durum wheat is the second most widely produced cereal in the world. Complex, large and unsequenced genomes, in addition to a lack of genomic resources, hinder the molecular characterization of tolerance mechanisms. This paper describes the isolation and characterization of five TdWRKY genes from durum wheat ( Triticum turgidum L . ssp. durum ). A PCR-based screening of a T. turgidum BAC genomic library using primers within the conserved region of WRKY genes resulted in the isolation of five BAC clones. Following sequencing fully the five BACs, fine annotation through Triannot pipeline revealed 74.6% of the entire sequences as transposable elements and a 3.2% gene content with genes organized as islands within oceans of TEs. Each BAC clone harbored a TdWRKY gene. The study showed a very extensive conservation of genomic structure between TdWRKYs and their orthologs from Brachypodium, barley, and T. aestivum . The structural features of TdWRKY proteins suggested that they are novel members of the WRKY family in durum wheat. TdWRKY1/2/4, TdWRKY3, and TdWRKY5 belong to the group Ia, IIa, and IIc, respectively. Enrichment of cis -regulatory elements related to stress responses in the promoters of some TdWRKY genes indicated their potential roles in mediating plant responses to a wide variety of environmental stresses. TdWRKY genes displayed different expression patterns in response to salt stress that distinguishes two durum wheat genotypes with contrasting salt stress tolerance phenotypes. TdWRKY genes tended to react earlier with a down-regulation in sensitive genotype leaves and with an up-regulation in tolerant genotype leaves. The TdWRKY transcripts levels in roots increased in tolerant genotype compared to sensitive genotype. The present results indicate that these genes might play some functional role in the salt tolerance in durum wheat.

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters.

PubMed

Wang, Wanfeng; Guo, Yanling; Yang, Qingxiang; Huang, Yao; Zhu, Chunyou; Fan, Jing; Pan, Feng

2015-07-15

Two biofilters were constructed using biological activated carbon (BAC) and nitrosamine-containing water from two drinking water treatment plants. The microbiome of each biofilter was characterized by 454 high-throughput pyrosequencing, and one nitrosamine-reducing bacterium was isolated. The results showed that nitrosamines changed the relative abundance at both the phylum and class levels, and the new genera were observed in the microbial communities of the two BAC filters after cultivation. As such, the genus Rhodococcus, which includes many nitrosamine-reducing strains reported in previous studies, was only detected in the BAC2 filter after cultivation. These findings indicate that nitrosamines can significantly affect the genus level in the microbial communities. Furthermore, the isolated bacterial culture Rhodococcus cercidiphylli A41 AS-1 exhibited the ability to reduce five nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine, N-nitrosodi-n-propylamine, N-nitrosopyrrolidine, and N-nitrosodi-n-butylamine) with removal ratios that ranged from 38.1% to 85.4%. The isolate exhibited a better biodegradation ability with nitrosamine as the carbon source when compared with nitrosamine as the nitrogen source. This study increases our understanding of the microbial community in drinking water biofilters with trace quantities of nitrosamines, and provides information on the metabolism of nitrosamine-reducing bacteria. Copyright © 2015. Published by Elsevier B.V.

Removal of arsenic and iron removal from drinking water using coagulation and biological treatment.

PubMed

Pramanik, Biplob Kumar; Pramanik, Sagor Kumar; Suja, Fatihah

2016-02-01

Effects of biological activated carbon (BAC), biological aerated filter (BAF), alum coagulation and Moringa oleifera coagulation were investigated to remove iron and arsenic contaminants from drinking water. At an initial dose of 5 mg/L, the removal efficiency for arsenic and iron was 63% and 58% respectively using alum, and 47% and 41% respectively using Moringa oleifera. The removal of both contaminants increased with the increase in coagulant dose and decrease in pH. Biological processes were more effective in removing these contaminants than coagulation. Compared to BAF, BAC gave greater removal of both arsenic and iron, removing 85% and 74%, respectively. Longer contact time for both processes could reduce the greater concentration of arsenic and iron contaminants. The addition of coagulation (at 5 mg/L dosage) and a biological process (with 15 or 60 min contact time) could significantly increase removal efficiency, and the maximum removal was observed for the combination of alum and BAC treatment (60 min contact time), with 100% and 98.56% for arsenic and iron respectively. The reduction efficiency of arsenic and iron reduced with the increase in the concentration of dissolved organics in the feedwater due to the adsorption competition between organic molecules and heavy metals.

Convergent evolution in the genetic basis of Müllerian mimicry in heliconius butterflies.

PubMed

Baxter, Simon W; Papa, Riccardo; Chamberlain, Nicola; Humphray, Sean J; Joron, Mathieu; Morrison, Clay; ffrench-Constant, Richard H; McMillan, W Owen; Jiggins, Chris D

2008-11-01

The neotropical butterflies Heliconius melpomene and H. erato are Müllerian mimics that display the same warningly colored wing patterns in local populations, yet pattern diversity between geographic regions. Linkage mapping has previously shown convergent red wing phenotypes in these species are controlled by loci on homologous chromosomes. Here, AFLP bulk segregant analysis using H. melpomene crosses identified genetic markers tightly linked to two red wing-patterning loci. These markers were used to screen a H. melpomene BAC library and a tile path was assembled spanning one locus completely and part of the second. Concurrently, a similar strategy was used to identify a BAC clone tightly linked to the locus controlling the mimetic red wing phenotypes in H. erato. A methionine rich storage protein (MRSP) gene was identified within this BAC clone, and comparative genetic mapping shows red wing color loci are in homologous regions of the genome of H. erato and H. melpomene. Subtle differences in these convergent phenotypes imply they evolved independently using somewhat different developmental routes, but are nonetheless regulated by the same switch locus. Genetic mapping of MRSP in a third related species, the "tiger" patterned H. numata, has no association with wing patterning and shows no evidence for genomic translocation of wing-patterning loci.

A dramatic increase in the positive blood culture rates of Helicobacter cinaedi: the evidence of differential detection abilities between the Bactec and BacT/Alert systems.

PubMed

Miyake, Noriko; Chong, Yong; Nishida, Ruriko; Nagasaki, Yoji; Kibe, Yasushi; Kiyosuke, Makiko; Shimomura, Takeshi; Shimono, Nobuyuki; Shimoda, Shinji; Akashi, Koichi

2015-11-01

In our hospital, positive blood culture rates of Helicobacter cinaedi dramatically increased after introducing the Bactec system. A simulated culture model of H. cinaedi bacteremia demonstrated no positive signals using the BacT/Alert system, despite efficient growth in bottles. Clinically suspected H. cinaedi bacteremia should be monitored more closely when using the BacT/Alert system, preferably with subcultivation after 7days of incubation. Copyright © 2015 Elsevier Inc. All rights reserved.

Functional movement impairment in dancers: An assessment and treatment approach utilizing the Biomechanical Asymmetry Corrector (BAC) to restore normal mechanics of the spine and pelvis.

PubMed

Keller, K; West, J C

1995-01-01

Musculoskeletal injuries to the spine and pelvis are common in dancers. These injuries are associated with mechanical dysfunctions that impair spinal adaptation to the movement demands of the art form. This article introduces the biomechanical asymmetry corrector (BAC), a dynamic assessment and treatment tool, designed to restore normal spinal mechanics and functional movement patterns in dancers. A discussion of lumbo-pelvic mechanics and dance injury provides a theoretical context for describing exercises on the BAC.

Transcriptome comparison in the pituitary-adrenal axis between Beagle and Chinese Field dogs after chronic stress exposure.

PubMed

Luo, Wei; Fang, Meixia; Xu, Haiping; Xing, Huijie; Nie, Qinghua

2015-10-01

Chronic stress can induce a series of maladjustments, and the response to stress is partly regulated by the hypothalamus-pituitary-adrenal axis. The aim of this study was to investigate the genetic mechanisms of this axis regulating stress responsiveness. The pituitary and adrenal cortex of Beagle and Chinese Field Dog (CFD) from a stress exposure group [including Beagle pituitary 1 (BP1), CFD pituitary 1 (CFDP1), Beagle adrenal cortex 1 (BAC1), CFD adrenal cortex 1 (CFDAC1)] and a control group [including Beagle pituitary 2 (BP2), CFD pituitary 2 (CFDP2), Beagle adrenal cortex 2 (BAC2), CFD adrenal cortex 2 (CFDAC2)], selected to perform RNA-seq transcriptome comparisons, showed that 40, 346, 376, 69, 70, 38, 57 and 71 differentially expressed genes were detected in BP1 vs. BP2, CFDP1 vs. CFDP2, BP1 vs. CFDP1, BP2 vs. CFDP2, BAC1 vs. BAC2, CFDAC1 vs. CFDAC2, BAC1 vs. CFDAC1 and BAC2 vs. CFDAC2 respectively. NPB was a gene common to BAC1 vs. BAC2 and CFDAC1 vs. CFDAC2, indicating it was a potential gene affecting response to chronic stress, regardless of the extent of chronic stress induced. PLP1 was a gene common to BP1 vs. CFDP1 and BP2 vs. CFDP2, suggesting its important roles in affecting the stress-tolerance difference between the two breeds, regardless of whether there was stress exposure or not. Pathway analysis found 12, 4, 11 and 1 enriched pathway in the comparisons of BP1 vs. CFDP1, BP2 vs. CFDP2, CFDP1 vs. CFDP2 and BAC1 vs. BAC2 respectively. Glutamatergic synapse, neuroactive ligand-receptor interaction, retrograde endocannabinoid signaling, GABAergic synapse, calcium signaling pathway and dopaminergic synapse were the most significantly enriched pathways in both CFDP1 vs. CFDP2 and BP1 vs. CFDP1. GO, KEGG pathway and gene network analysis demonstrated that GRIA3, GRIN2A, GRIN2B and NPY were important in regulating the stress response in CFD. Nevertheless, ADORA1, CAMK2A, GRM1, GRM7 and NR4A1 might be critical genes contributing to the stress-tolerance difference between CFD and Beagle when subjected to stress exposure. In addition, RGS4 and SYN1 might play important roles both in regulating the stress response in CFD and in affecting the stress-tolerance difference in different breeds. These observations clearly showed that some genes in the adrenal cortex and pituitary could regulate the stress response in Beagle and CFDs, whereas some others could affect the stress-tolerance difference between these two breeds. Our results can contribute to a more comprehensive understanding of the genetic mechanisms of response to chronic stress. © 2015 Stichting International Foundation for Animal Genetics.

Silurian and Devonian in Vietnam—Stratigraphy and facies

NASA Astrophysics Data System (ADS)

Thanh, Tống Duy; Phương, Tạ Hoàng; Janvier, Philippe; Hùng, Nguyễn Hữu; Cúc, Nguyễn Thị Thu; Dương, Nguyễn Thùy

2013-09-01

Silurian and Devonian deposits in Viet Nam are present in several zones and regions, including Quang Ninh, East Bac Bo, and West Bac Bo Zones of the Bac Bo Region, the Dien Bien-Nghe An and Binh Tri Thien Zones of the Viet-Lao Region, and the South Trung Bo, and Western Nam Bo Zones of the South Viet Nam Region (Fig. 1). The main lithological features and faunal composition of the Silurian and Devonian Units in all these zones are briefly described. The Silurian consists of deep-water deposits of the upper parts of the Co To and Tan Mai Formations in the Quang Ninh Zone, the upper parts of the Phu Ngu Formation in the East Bac Bo Zone and the upper parts of the Long Dai and Song Ca Formations in the Viet-Lao Region. Shallow water facies Silurian units containing benthic faunas are more widely distributed, including the upper part of the Sinh Vinh and Bo Hieng Formations in the West Bac Bo Zone, the Kien An Formation in the Quang Ninh Zone, and, in the Viet-Lao Region, the Dai Giang Formation and the upper part of the Tay Trang Formation. No Lower and Middle Devonian deposits indicate deep water facies, but they are characterized by different shallow water facies. Continental to near shore, deltaic facies characterize the Lower Devonian Song Cau Group in the East Bac Bo Zone, the Van Canh Formation in the Quang Ninh Zone, and the A Choc Formation in the Binh Tri Thien Zone. Similar facies also occur in the Givetian Do Son Formation of the Quang Ninh Zone, and the Tan Lap Formation in the East Bac Bo Zone, and consist of coarse terrigenous deposits—cross-bedded conglomerates, sandstone, etc. Most Devonian units are characterized by shallow marine shelf facies. Carbonate and terrigenous-carbonate facies dominate, and terrigenous facies occur in the Lower and Middle Devonian sections in some areas only. The deep-water-like facies is characteriztic for some Upper Devonian formations in the Bac Bo (Bang Ca and Toc Tat Formations) and Viet-Lao Regions (Thien Nhan and Xom Nha Formations). These formations contain cherty shale or siliceous limestone, and fossils consist of conodonts, but there are also brachiopods and other benthos. They were possibly deposited in a deep water environment on the slope of the continental shelf. Most Devonian units distributed in the North and the Central Viet Nam consist of self shallow water sediments, and apparently they were deposited in a passive marginal marine environment. The coarse clastic continental or subcontinental deposits are distributed only in some areas of the East Bac Bo and of the Quang Ninh zones of the Bac Bo Region, and in the south of the Binh Tri Thien Zone. This situation suggests the influence of the Caledonian movement at the end of the Silurian period that called the Guangxi movement in South China.

Methods for estimating expected blood alcohol concentration.

DOT National Transportation Integrated Search

1980-12-01

Estimates of blood alcohol concentration (BAC) typically are based on the amount of alcohol consumed per pound body weight. This method fails to consider food intake and body composition, which significantly affect BAC. A laboratory experiment was co...

Methods for estimating expected blood alcohol concentration

DOT National Transportation Integrated Search

1980-08-01

Estimates of blood alcohol concentration (BAC) typically are based on the amount of alcohol consumed per pound bodyweight. This method fails to consider either food intake or body composition, factors which significantly affect BAC. A laboratory expe...

14 CFR 91.1505 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... operate an Airbus Model A300 (excluding the -600 series), British Aerospace Model BAC 1-11, Boeing Model... below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight cycle...

14 CFR 91.1505 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... operate an Airbus Model A300 (excluding the -600 series), British Aerospace Model BAC 1-11, Boeing Model... below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight cycle...

14 CFR 91.1505 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... operate an Airbus Model A300 (excluding the -600 series), British Aerospace Model BAC 1-11, Boeing Model... below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight cycle...

Bacterial Artificial Chromosome Clones of Viruses Comprising the Towne Cytomegalovirus Vaccine

PubMed Central

Cui, Xiaohong; Adler, Stuart P.; Davison, Andrew J.; Smith, Larry; Habib, EL-Sayed E.; McVoy, Michael A.

2012-01-01

Bacterial artificial chromosome (BAC) clones have proven invaluable for genetic manipulation of herpesvirus genomes. BAC cloning can also be useful for capturing representative genomes that comprise a viral stock or mixture. The Towne live attenuated cytomegalovirus vaccine was developed in the 1970s by serial passage in cultured fibroblasts. Although its safety, immunogenicity, and efficacy have been evaluated in nearly a thousand human subjects, the vaccine itself has been little studied. Instead, genetic composition and in vitro growth properties have been inferred from studies of laboratory stocks that may not always accurately represent the viruses that comprise the vaccine. Here we describe the use of BAC cloning to define the genotypic and phenotypic properties of viruses from the Towne vaccine. Given the extensive safety history of the Towne vaccine, these BACs provide a logical starting point for the development of next-generation rationally engineered cytomegalovirus vaccines. PMID:22187535

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

PubMed Central

Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao-Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Daniel; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, Saki; Muñoz-Amatriaín, María; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Houben, Andreas; Doležel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin

2017-01-01

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX). PMID:28448065

Bacterial artificial chromosome clones of viruses comprising the towne cytomegalovirus vaccine.

PubMed

Cui, Xiaohong; Adler, Stuart P; Davison, Andrew J; Smith, Larry; Habib, El-Sayed E; McVoy, Michael A

2012-01-01

Bacterial artificial chromosome (BAC) clones have proven invaluable for genetic manipulation of herpesvirus genomes. BAC cloning can also be useful for capturing representative genomes that comprise a viral stock or mixture. The Towne live attenuated cytomegalovirus vaccine was developed in the 1970s by serial passage in cultured fibroblasts. Although its safety, immunogenicity, and efficacy have been evaluated in nearly a thousand human subjects, the vaccine itself has been little studied. Instead, genetic composition and in vitro growth properties have been inferred from studies of laboratory stocks that may not always accurately represent the viruses that comprise the vaccine. Here we describe the use of BAC cloning to define the genotypic and phenotypic properties of viruses from the Towne vaccine. Given the extensive safety history of the Towne vaccine, these BACs provide a logical starting point for the development of next-generation rationally engineered cytomegalovirus vaccines.

Microbial source tracking and transfer hydrodynamics in rural catchments.

NASA Astrophysics Data System (ADS)

Murphy, Sinead; Bhreathnach, Niamh; O'Flaherty, Vincent; Jordan, Philip; Wuertz, Stefan

2013-04-01

In Ireland, bacterial pathogens from continual point source pollution and intermittent pollution from diffuse sources can impact both drinking water supplies and recreational waters. This poses a serious public health threat. Observing and establishing the source of faecal pollution is imperative for the protection of water quality and human health. Traditional culture methods to detect such pollution via faecal indicator bacteria have been widely utilised but do not decipher the source of pollution. To combat this, microbial source tracking, an important emerging molecular tool, is applied to detect host-specific markers in faecally contaminated waters. The aim of this study is to target ruminant and human-specific faecal Bacteroidales and Bacteroides 16S rRNA genes within rural river catchments in Ireland and investigate hydrological transfer dependencies. During storm events and non-storm periods, 1L untreated water samples, taken every 2 hours over a 48-hour time period at the spring (Cregduff) or outlet (Dunleer), and large (5-20L) untreated water samples were collected from two catchment sites. Cregduff is a spring emergence under a grassland karst landscape in Co. Mayo (west coast of Ireland) and Dunleer is a mixed landuse over till soils in Co. Louth (east coast). From a risk assessment point of view, the catchments are very different. Samples were filtered through 0.2µm nitrocellulose filters to concentrate bacterial cells which then underwent chemical extraction of total nucleic acids. Animal and human stool samples were also collected from the catchments to determine assay sensitivity and specificity following nucleic acid extraction. Aquifer response to seasonal events was assessed by monitoring coliforms and E. coli occurrence using the IDEXX Colisure® Quanti Tray®/2000 system in conjunction with chemical and hydrological parameters. Autoanalysers deployed at each catchment monitor multiple water parameters every 10 min such as phosphorus, nitrogen (nitrate), turbidity, conductivity and flow rate. InStat V 3.06 was used to determine correlations between chemical and microbial parameters (P< 0.05 considered significant).There was a positive correlation between E. coli and phosphorus in Cregduff during rain events (p=0.040) & significant correlation for a non-rain periods (<0.001). There was a positive correlation between E. coli and turbidity in Dunleer during rain events (p=0.0008) and in Cregduff during non-rain periods (p=0.0241). The water samples from Dunleer have a higher concentration of phosphorus than in Cregduff. Host specific primers BacCow-UCD, BacHum-UCD, BacUni-UCD and BoBac were then assayed against both faecal and water extracts and quantified using PCR. BacUni-UCD, BacCow-UCD and BoBac detected faecal contamination in three of the four sample sites in Dunleer and BacHum-UCD detected faecal contamination in one of the sites. The concentrations of the BacUni-UCD qPCR assay were higher in the water samples taken from Dunleer outlet than those taken from Cregduff spring. BacCow-UCD and BacHum-UCD qPCR detected low and very low concentrations, respectively, in water from the Dunleer outlet. The concentrations can be seen changing over the hydrograph event. None of the host-specific assays detected pollution in Cregduff. From the results, it can be seen that Dunleer is more subject to contamination than Cregduff.

General deterrence effects of U.S. statutory DUI fine and jail penalties: long-term follow-up in 32 states.

PubMed

Wagenaar, Alexander C; Maldonado-Molina, Mildred M; Erickson, Darin J; Ma, Linan; Tobler, Amy L; Komro, Kelli A

2007-09-01

We examined effects of state statutory changes in DUI fine or jail penalties for firsttime offenders from 1976 to 2002. A quasi-experimental time-series design was used (n=324 monthly observations). Four outcome measures of drivers involved in alcohol-related fatal crashes are: single-vehicle nighttime, low BAC (0.01-0.07g/dl), medium BAC (0.08-0.14g/dl), high BAC (>/=0.15g/dl). All analyses of BAC outcomes included multiple imputation procedures for cases with missing data. Comparison series of non-alcohol-related crashes were included to efficiently control for effects of other factors. Statistical models include state-specific Box-Jenkins ARIMA models, and pooled general linear mixed models. Twenty-six states implemented mandatory minimum fine policies and 18 states implemented mandatory minimum jail penalties. Estimated effects varied widely from state to state. Using variance weighted meta-analysis methods to aggregate results across states, mandatory fine policies are associated with an average reduction in fatal crash involvement by drivers with BAC>/=0.08g/dl of 8% (averaging 13 per state per year). Mandatory minimum jail policies are associated with a decline in single-vehicle nighttime fatal crash involvement of 6% (averaging 5 per state per year), and a decline in low-BAC cases of 9% (averaging 3 per state per year). No significant effects were observed for the other outcome measures. The overall pattern of results suggests a possible effect of mandatory fine policies in some states, but little effect of mandatory jail policies.

Determination of quaternary ammonium compounds in oranges and cucumbers using QuEChERS extraction and ultra-performance liquid chromatography/tandem mass spectrometry.

PubMed

Arrebola-Liébanas, Francisco Javier; Abdo, María Angeles Herrera; Moreno, José Luis Fernandez; Martínez-Vidal, José L; Frenich, Antonia Garrido

2014-01-01

A simple and fast method has been developed for determining relevant quaternary ammonium compounds in cucumber and orange samples. The target compounds were benzoalkonium chloride (BAC-10, BAC-12, BAC-14, and BAC-16), didecyldimethylammonium chloride, and benzethonium chloride, all frequently used biocides in the agrifood industry. An extraction based on the buffered Quick, Easy, Cheap, Effective, Rugged, and Safe method and determination by ultra-performance LC/MS/MS that eluted the biocides in less than 5 min were used. The method was fully validated and implemented in a UNE-EN-ISO/IEC 17025 accredited laboratory for its application to the analysis of real samples. Performance characteristics of the method are reported, including an estimation of measurement uncertainty. Calibration curves were set between 0.01 and 0.150 mg/kg, LOD values were always between 0.4 and 1.0 microg/kg, LOQ values were in the range 1-4 microg/kg, recovery was between 81 and 115%, intraday and interday precision were always lower than 17% (expressed as RSD), and expanded uncertainty was always lower than 40%. The validation was accomplished for the two studied matrixes at spiking concentrations of 0.011 and 0.050 mg/kg. The method has been applied to the analysis of 30 cucumber and orange samples that were found to contain concentrations of BAC-12 that ranged between 0.015 and 0.210 mg/kg and of BAC-14 between 0.018 and 0.081 mg/kg.

Removing organic and nitrogen content from a highly saline municipal wastewater reverse osmosis concentrate by UV/H2O2-BAC treatment.

PubMed

Pradhan, Shovana; Fan, Linhua; Roddick, Felicity A

2015-10-01

Reverse osmosis (RO) concentrate (ROC) streams generated from RO-based municipal wastewater reclamation processes pose potential health and environmental risks on their disposal to confined water bodies such as bays. A UV/H2O2 advanced oxidation process followed by a biological activated carbon (BAC) treatment was evaluated at lab-scale for the removal of organic and nutrient content from a highly saline ROC (TDS 16 g L(-1), EC 23.5 mS cm(-1)) for its safe disposal to the receiving environment. Over the 230-day operation of the UV/H2O2-BAC process, the colour and UV absorbance (254 nm) of the ROC were reduced to well below those of the influent to the reclamation process. The concentrations of DOC and total nitrogen (TN) were reduced by approximately 60% at an empty bed contact time (EBCT) of 60 min. The reduction in ammonia nitrogen by the BAC remained high under all conditions tested (>90%). Further investigation confirmed that the presence of residual peroxide in the UV/H2O2 treated ROC was beneficial for DOC removal, but markedly inhibited the activities of the nitrifying bacteria (i.e., nitrite oxidising bacteria) in the BAC system and hence compromised total nitrogen removal. This work demonstrated that the BAC treatment could be acclimated to the very high salinity environment, and could be used as a robust method for the removal of organic matter and nitrogen from the pre-oxidised ROC under optimised conditions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Technical note: Could benzalkonium chloride be a suitable alternative to mercuric chloride for preservation of seawater samples?

NASA Astrophysics Data System (ADS)

Gloël, J.; Robinson, C.; Tilstone, G. H.; Tarran, G.; Kaiser, J.

2015-12-01

Instrumental equipment unsuitable or unavailable for fieldwork as well as lack of ship space can necessitate the preservation of seawater samples prior to analysis in a shore-based laboratory. Mercuric chloride (HgCl2) is routinely used for such preservation, but its handling and subsequent disposal incur environmental risks and significant expense. There is therefore a strong motivation to find less hazardous alternatives. Benzalkonium chloride (BAC) has been used previously as microbial inhibitor for freshwater samples. Here, we assess the use of BAC for marine samples prior to the measurement of oxygen-to-argon (O2 / Ar) ratios, as used for the determination of biological net community production. BAC at a concentration of 50 mg dm-3 inhibited microbial activity for at least 3 days in samples tested with chlorophyll a (Chl a) concentrations up to 1 mg m-3. BAC concentrations of 100 and 200 mg dm-3 were no more effective than 50 mg dm-3. With fewer risks to human health and the environment, and no requirement for expensive waste disposal, BAC could be a viable alternative to HgCl2 for short-term preservation of seawater samples, but is not a replacement for HgCl2 in the case of oxygen triple isotope analysis, which requires storage over weeks to months. In any event, further tests on a case-by-case basis should be undertaken if use of BAC was considered, since its inhibitory activity may depend on concentration and composition of the microbial community.

Theobroma cacao: A genetically integrated physical map and genome-scale comparative synteny analysis

USDA-ARS?s Scientific Manuscript database

A comprehensive integrated genomic framework is considered a centerpiece of genomic research. In collaboration with the USDA-ARS (SHRS) and Mars Inc., the Clemson University Genomics Institute (CUGI) has developed a genetically anchored physical map of the T. cacao genome. Three BAC libraries contai...

14 CFR 125.505 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2011 CFR

2011-01-01

... operate an Airbus Model A300 (exlcuding the -600 series), British Aerospace Model BAC 1-11, Boeing Model...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

14 CFR 121.1107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Airbus Model A300 (excluding the -600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

14 CFR 129.107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Model A300 (excluding −600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720, 727, 737... all models of the British Aerospace BAC 1-11, the flight cycle implementation time is 60,000 flights...

14 CFR 125.505 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... operate an Airbus Model A300 (exlcuding the -600 series), British Aerospace Model BAC 1-11, Boeing Model...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

14 CFR 129.107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Model A300 (excluding −600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720, 727, 737... all models of the British Aerospace BAC 1-11, the flight cycle implementation time is 60,000 flights...

14 CFR 129.107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Model A300 (excluding −600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720, 727, 737... all models of the British Aerospace BAC 1-11, the flight cycle implementation time is 60,000 flights...

14 CFR 125.505 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... operate an Airbus Model A300 (exlcuding the -600 series), British Aerospace Model BAC 1-11, Boeing Model...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

14 CFR 121.1107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Airbus Model A300 (excluding the -600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

14 CFR 121.1107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Airbus Model A300 (excluding the -600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

14 CFR 129.107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Model A300 (excluding −600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720, 727, 737... all models of the British Aerospace BAC 1-11, the flight cycle implementation time is 60,000 flights...

14 CFR 121.1107 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Airbus Model A300 (excluding the -600 series), British Aerospace Model BAC 1-11, Boeing Model 707, 720...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

14 CFR 125.505 - Repairs assessment for pressurized fuselages.

Code of Federal Regulations, 2012 CFR

2012-01-01

... operate an Airbus Model A300 (exlcuding the -600 series), British Aerospace Model BAC 1-11, Boeing Model...,000 flights below the window line. (2) For all models of the British Aerospace BAC 1-11, the flight...

Driver characteristics and impairment at various BACs

DOT National Transportation Integrated Search

2000-08-01

The purpose of this experiment was to determine (a) the magnitude of alcohol impairment of driving skills as blood alcohol concentrations (BACs) varied from zero to 0.10% and (b) whether age, gender, and drinking practice characteristics of the subje...

Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species

PubMed Central

Wu, Chengcang; Proestou, Dina; Carter, Dorothy; Nicholson, Erica; Santos, Filippe; Zhao, Shaying; Zhang, Hong-Bin; Goldsmith, Marian R

2009-01-01

Background Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date. Results We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the H. erato genome is somewhat more abundant in repeat elements and simple repeats than those of M. sexta and H. virescens. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of H. virescens being the most conserved as a typical lepidopteran, whereas both genomes of H. erato and M. sexta appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences. Conclusion The high-quality and large-insert BAC libraries of the insects, together with the identified BACs containing genes of interest, provide valuable information, resources and tools for comprehensive understanding and studies of the insect genomes and for addressing many fundamental questions in Lepidoptera. The sample of the genomic sequences provides the first insight into the constitution and evolution of the insect genomes. PMID:19558662

Use of carbon steel ball bearings to determine the effect of biocides and corrosion inhibitors on microbiologically influenced corrosion under flow conditions.

PubMed

Pinnock, Tijan; Voordouw, Johanna; Voordouw, Gerrit

2018-05-10

A consortium of sulfate-reducing bacteria consisting mostly of Desulfovibrio, Desulfomicrobium, and Desulfocurvus from oil field produced water was cultivated in a chemostat, receiving medium with 20 mM formate and 10 mM sulfate as the energy and 1 mM acetate as the carbon source. The chemostat effluent, containing 5 mM sulfide and 0.5 mM of residual acetate, was passed through 1-ml syringe columns with 60 carbon steel ball bearings (BBs) of 53.6 ± 0.1 mg each at a flow rate of 0.8 ml/h per column. These were treated every 5 days with 1.6 ml of 300 ppm of glutaraldehyde (Glut), tetrakis(hydroxymethyl)phosphonium sulfate (THPS), benzalkonium chloride (BAC), or Glut/BAC, a mixture of Glut and BAC. Alternatively, BBs were treated with 33% (v/v) of a water-soluble (CR_W) or an oil-soluble (CR_O1 or CR_O3) corrosion inhibitor for 20 s after which the corrosion inhibitor was drained off and BBs were packed into columns. The effluent of untreated control columns had no acetate. Treatment with the chemically reactive biocides Glut and THPS, as well as with Glut/BAC, gave a transient increase of acetate indicating decreased microbial activity. This was not seen with BAC alone indicating it to be the least effective biocide. Relative to untreated BBs (100%), those treated periodically with Glut, THPS, BAC, or Glut/BAC had a general weight loss corrosion rate of 91, 81, 45, and 36% of the untreated rate of 0.104 ± 0.004 mm/year, respectively. Single treatment with corrosion inhibitors decreased corrosion to 48, 2, and 1% of the untreated rate for CR_W, CR_O1 and CR_O3, respectively. Analysis of the distribution of corrosion rates from the weight loss of individual BBs (N = 120) indicated the presence of a more slowly and a more rapidly corroding group. BAC treatment prevented emergence of the latter, and this quaternary ammonium detergent appeared most effective in decreasing corrosion not because of its biocidal properties, but because of its corrosion inhibitory properties.

0.08 BAC Illegal Per Se Level

DOT National Transportation Integrated Search

1996-09-01

The U.S. Department of Transportation's National Highway Traffic Safety Administration (NHTSA) encourages States to have laws that make it illegal for a person to operate a motor vehicle if he or she has blood or breath alcohol concentration (BAC) of...

BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

NASA Astrophysics Data System (ADS)

Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

2012-05-01

Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

piggyBac Transposon-Mediated Transgenesis in the Apicomplexan Parasite Eimeria tenella

PubMed Central

Su, Huali; Liu, Xianyong; Yan, Wenchao; Shi, Tuanyuan; Zhao, Xinxin; Blake, Damer P.; Tomley, Fiona M.; Suo, Xun

2012-01-01

piggyBac, a type II transposon that is useful for efficient transgenesis and insertional mutagenesis, has been used for effective and stable transfection in a wide variety of organisms. In this study we investigate the potential use of the piggyBac transposon system for forward genetics studies in the apicomplexan parasite Eimeria tenella. Using the restriction enzyme-mediated integration (REMI) method, E. tenella sporozoites were electroporated with a donor plasmid containing the enhanced yellow fluorescent protein (EYFP) gene flanked by piggyBac inverted terminal repeats (ITRs), an Asc I-linearized helper plasmid containing the transposase gene and the restriction enzyme Asc I. Subsequently, electroporated sporozoites were inoculated into chickens via the cloacal route and transfected progeny oocysts expressing EYFP were sorted by flow cytometry. A transgenic E. tenella population was selected by successive in vivo passage. Southern-blotting analysis showed that exogenous DNA containing the EYFP gene was integrated into the parasite genome at a limited number of integration sites and that the inserted part of the donor plasmid was the fragment located between the 5′ and 3′ ITRs as indicated by primer-specific PCR screening. Genome walking revealed that the insertion sites were TTAA-specific, which is consistent with the transposition characteristics of piggyBac. PMID:22768223

Short-term microbial release during rain events from on-site sewers and cattle in a surface water source.

PubMed

Aström, Johan; Pettersson, Thomas J R; Reischer, Georg H; Hermansson, Malte

2013-09-01

The protection of drinking water from pathogens such as Cryptosporidium and Giardia requires an understanding of the short-term microbial release from faecal contamination sources in the catchment. Flow-weighted samples were collected during two rainfall events in a stream draining an area with on-site sewers and during two rainfall events in surface runoff from a bovine cattle pasture. Samples were analysed for human (BacH) and ruminant (BacR) Bacteroidales genetic markers through quantitative polymerase chain reaction (qPCR) and for sorbitol-fermenting bifidobacteria through culturing as a complement to traditional faecal indicator bacteria, somatic coliphages and the parasitic protozoa Cryptosporidium spp. and Giardia spp. analysed by standard methods. Significant positive correlations were observed between BacH, Escherichia coli, intestinal enterococci, sulphite-reducing Clostridia, turbidity, conductivity and UV254 in the stream contaminated by on-site sewers. For the cattle pasture, no correlation was found between any of the genetic markers and the other parameters. Although parasitic protozoa were not detected, the analysis for genetic markers provided baseline data on the short-term faecal contamination due to these potential sources of parasites. Background levels of BacH and BacR makers in soil emphasise the need to including soil reference samples in qPCR-based analyses for Bacteroidales genetic markers.

Synthesis and Examination of Nanocomposites Based on Poly(2-hydroxyethyl methacrylate) for Medicinal Use

NASA Astrophysics Data System (ADS)

Kukolevska, Olena S.; Gerashchenko, Igor I.; Borysenko, Mykola V.; Pakhlov, Evgenii M.; Machovsky, Michal; Yushchenko, Tetyana I.

2017-02-01

Preparation of poly(2-hydroxyethyl methacrylate) (PHEMA) based nanocomposites using different approaches such as synthesis with water as the porogen, filling of polymer matrix by silica and formation of interpenetrating polymer networks with polyurethane was demonstrated. Incorporation of various biologically active compounds (BAC) such as metronidazole, decamethoxin, zinc sulphate, silver nitrate or amino acids glycine and tryptophan into nanocomposites was achieved. BAC were introduced into the polymer matrix either (1) directly, or (2) with a solution of colloidal silica, or (3) through immobilization on silica (sol-densil). Morphology of prepared materials was investigated by laser scanning microscopy and low-vacuum scanning electron microscopy. In vacuum freeze-drying, prior imaging was proposed for improving visualization of the porous structure of composites. The interaction between PHEMA matrix and silica filler was investigated by IR spectroscopy. Adsorption of 2-hydroxyethyl methacrylate and BAC from aqueous solution on the silica surface was also examined. Phase composition and thermal stability of composites were studied by the differential thermogravimetry/differential thermal analysis. Release of BAC into water medium from prepared composites were shown to depend on the synthetic method and differed significantly. Obtained PHEMA-base materials which are characterized by controlled release of BAC have a strong potential for application in manufacturing of different surgical devices like implants, catheters and drainages.

Morphological and functional changes after benzalkonium chloride treatment of the small intestinal Thiry-Vella loop in rats.

PubMed

Móricz, K; Gyetvai, B; Bárdos, G

1998-08-01

The aim of this work was to study the effects of benzalkonium chloride (BAC) treatment on the small intestine and its functioning in rats surgically prepared with Thiry-Vella intestinal loop. The loops were treated with either BAC, which ablated much of the myenteric plexus and extrinsic innervation, or with physiological saline (SAL). In vivo drinking experiments were performed to examine the effect on fluid intake and behavioral indices of distending the loop with a balloon. Spontaneous motility and its changes induced by acetylcholine (ACh) and histamine (His) were studied on isolated stripes in vitro. Finally, samples from the loops were examined histologically. Though reduction of the cell number was less than expected and no differences of the thickness of the muscular layer between the two groups was observed, BAC treatment altered the pattern of spontaneous activity and also the sensitivity to ACh and His in isolated stripes. In vivo distension of the SAL-treated loops reduced fluid intake and produced signs of aversivity; these effects were absent in the BAC-treated group. Our results show that despite the differences in the degree of ablation from those obtained by others, BAC treatment can be used to study the mechanisms underlying the effects of the enteral stimuli on the behavior.

The detection of DWI at BACs below 0.10

DOT National Transportation Integrated Search

1997-09-01

The objective of the research described in this report has been to develop training materials to assist law enforcement officers in the accurate detection of motorists who are driving while impaired (DWI) at the 0.08 BAC level. The project was compos...

Bis(amino)cyclopropenylidene (BAC) catalyzed aza-benzoin reaction.

PubMed

Wilde, Myron M D; Gravel, Michel

2014-10-17

A bis(amino)cyclopropenylidene (BAC) catalyzed aza-benzoin reaction between aldehydes and phosphinoyl imines has been developed. The reaction is general with a wide range of aromatic aldehydes and aromatic imines. The reaction displays excellent chemoselectivity favoring aza-benzoin products over homobenzoin products.

The effects of 0.08 BAC laws

DOT National Transportation Integrated Search

1999-03-01

Straightforward and powerful reasons exist for lowering the legal limit of blood alcohol concentration (BAC) from 0.10 to 0.08. In 1964, Borkenstein et al. showed that drivers who had been drinking were more likely to be involved in a crash than sobe...

Local anesthetic inhibition of a bacterial sodium channel

PubMed Central

Lee, Sora; Goodchild, Samuel J.

2012-01-01

Recent structural breakthroughs with the voltage-gated sodium channel from Arcobacter butzleri suggest that such bacterial channels may provide a structural platform to advance the understanding of eukaryotic sodium channel gating and pharmacology. We therefore set out to determine whether compounds known to interact with eukaryotic NaVs could also inhibit the bacterial channel from Bacillus halodurans and NaChBac and whether they did so through similar mechanisms as in their eukaryotic homologues. The data show that the archetypal local anesthetic (LA) lidocaine inhibits resting NaChBac channels with a dissociation constant (Kd) of 260 µM, and channels displayed a left-shifted steady-state inactivation gating relationship in the presence of the drug. Extracellular application of QX-314 to expressed NaChBac channels had no effect on sodium current, whereas internal exposure via injection of a bolus of the quaternary derivative rapidly reduced sodium conductance, consistent with a hydrophilic cytoplasmic access pathway to an internal binding site. However, the neutral derivative benzocaine applied externally inhibited NaChBac channels, suggesting that hydrophobic pathways can also provide drug access to inhibit channels. Alternatively, ranolazine, a putative preopen state blocker of eukaryotic NaVs, displayed a Kd of 60 µM and left-shifted the NaChBac activation-voltage relationship. In each case, block enhanced entry into the inactivated state of the channel, an effect that is well described by a simple kinetic scheme. The data suggest that although significant differences exist, LA block of eukaryotic NaVs also occurs in bacterial sodium channels and that NaChBac shares pharmacological homology to the resting state of vertebrate NaV homologues. PMID:22641643

Six years' experience of using the BacT/ALERT system to screen all platelet concentrates, and additional testing of outdated platelet concentrates to estimate the frequency of false-negative results.

PubMed

Larsen, C P; Ezligini, F; Hermansen, N O; Kjeldsen-Kragh, J

2005-02-01

Approximately 1 in every 2000 units of platelets is contaminated with bacteria. The BacT/ALERT automated blood culture system can be used to screen platelet concentrates (PCs) for bacterial contamination. Data were collected from May 1998 until May 2004. The number of PCs tested during this period was 36 896, most of which were produced from pools of four buffy-coats. On the day following blood collection or platelet apheresis, a 5-10 ml sample of the PC was aseptically transferred to a BacT/ALERT culture bottle for detection of aerobic bacteria. The sample was monitored for bacterial growth during the entire storage period of the PC (6.5 days). When a positive signal was generated, the culture bottle, the PC and the erythrocyte concentrates were tested for bacterial growth. In order to determine the frequency of false-negative BacT/ALERT signals, 1061 outdated PCs were tested during the period from May 2002 to May 2004. Eighty-eight positive signals were detected by the BacT/ALERT system, of which 12 were interpreted as truly positive. Fourteen signals were interpreted as truly false positive. Thirty-three signals were interpreted to be probably false positive. Two of 1061 outdated units tested positive, and Bacillus spp. and Staphylococcus epidermidis, respectively, were isolated from these PCs. Between 0.03% and 0.12% of the PCs were contaminated with bacteria. BacT/ALERT is an efficient tool for monitoring PCs for bacterial contamination; however, it is important to realize that false-negative results may occur.

Spontaneous bacteriocin resistance in Listeria monocytogenes as a susceptibility screen for identifying different mechanisms of resistance and modes of action by bacteriocins of lactic acid bacteria.

PubMed

Macwana, Sunita; Muriana, Peter M

2012-01-01

A practical system was devised for grouping bacteriocins of lactic acid bacteria (LAB) based on mode of action as determined by changes in inhibitory activity to spontaneously-acquired bacteriocin resistance (Bac(R)). Wild type Listeria monocytogenes 39-2 was sensitive to five bacteriocins produced by 3 genera of LAB: pediocin PA-1 and pediocin Bac3 (Pediococcus), lacticin FS97 and lacticin FS56 (Lactococcus), and curvaticin FS47 (Lactobacillus). A spontaneous Bac(R) derivative of L. monocytogenes 39-2 obtained by selective recovery against lacticin FS56 provided complete resistance to the bacteriocin made by Lactococcus lactis FS56. The lacticin FS56-resistant strain of L. monocyotgenes 39-2 was also cross-resistant to curvaticin FS47 and pediocin PA-1, but not to lacticin FS97 or pediocin Bac3. The same pattern of cross-resistance was also observed with Bac(R) isolates obtained with L. monocytogenes Scott A-2. A spontaneous mutation that renders a strain cross-resistant to different bacteriocins indicates that they share a common mechanism of resistance due to similar modes of action of the bacteriocins. Spontaneous resistance was acquired to other bacteriocins (in aggregate) by following the same procedure against which the Bac(R) strain was still sensitive. In subsequent challenge assays, mixtures of bacteriocins of different modes of action provided greater inhibition than mixtures of bacteriocins of the same mode of action (as determined by our screening method). This study identifies a methodical approach to classify bacteriocins into functional groups based on mechanism of resistance (i.e., mode of action) that could be used for identifying the best mixture of bacteriocins for use as biopreservatives. Copyright © 2011 Elsevier B.V. All rights reserved.

Protective effects of carbenoxolone, an 11β-HSD1 inhibitor, against chemical induced dry eye syndrome.

PubMed

Na, Yoon-Ju; Choi, Kyoung-Jin; Park, Sung Bum; Sung, Hye-Rim; Jung, Won Hoon; Kim, Hee Youn; Rhee, Sang Dal; Kim, Ki Young

2017-11-01

Dry eye syndrome (DES) is a disorder of the eye due to tear deficiency or excessive evaporation that causes damage to the eye and is associated with discomfort and dryness. 11β-Hydroxysteroid dehydrogenase 1 (11β-HSD1) is an enzyme that converts inactive cortisone to active cortisol. Recently, 11β-HSD1 has been expressed in human and rodent eyes and has been recognized as a target of glaucoma. In this study, the therapeutic effects and underlying mechanisms of topical carbenoxolone, an 11β-HSD1 inhibitor, were investigated in benzalkonium chloride (BAC)-treated human conjunctival epithelial cells and a rat DES model. In the in vitro study, carbenoxolone dose-dependently inhibited cell death and 11β-HSD1 activity in BAC-treated human conjunctival epithelial cells. For the in vivo study, carbenoxolone or a solvent was administered to the BAC-induced DES model twice daily. BAC-treated rat eyes showed significant increases in ocular surface damage, a reduction of tears, decrease corneal thickness, corneal basement membrane destruction, apoptosis in the conjunctival epithelium, and expression of pro-inflammatory cytokines (TNF-α and IL-6) and 11β-HSD1. These effects of BAC were reversed by topical carbenoxolone treatment. These results demonstrate that carbenoxolone can prevent DES by inhibiting pro-inflammatory cytokine expression and cell death of the corneal and conjunctival epithelium via inhibition of both 11β-HSD1 activity and expression in the eyes of BAC-treated rats. It is suggested that topical 11β-HSD1 inhibitors may provide a new therapeutic window in the prevention and/or treatment of DES.